Method for using gene expression to determine prognosis of prostate cancer

ABSTRACT

The present disclosure includes assays that involve measurement of expression levels of prognostic biomarkers, or co-expressed biomarkers, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likely prognosis for the patient, and likelihood that the patient will have a recurrence of prostate cancer, or to classify the tumor by likelihood of clinical outcome or TMPRSS2 fusion status.

This application is a continuation of U.S. application Ser. No.16/282,540, filed Feb. 22, 2019, which is a continuation of U.S.application Ser. No. 14/887,605, filed Oct. 20, 2015, now U.S. Pat. No.10,260,104, issued Apr. 16, 2019, which is a continuation of U.S.application Ser. No. 13/190,391, filed Jul. 25, 2011, which claims thebenefit of priority to U.S. Provisional Application Nos. 61/368,217,filed Jul. 27, 2010; 61/414,310, filed Nov. 16, 2010; and 61/485,536,filed May 12, 2011, all of which are hereby incorporated by reference.

TECHNICAL FIELD

The present disclosure relates to molecular diagnostic assays thatprovide information concerning methods to use gene expression profilesto determine prognostic information for cancer patients. Specifically,the present disclosure provides genes and microRNAs, the expressionlevels of which may be used to determine the likelihood that a prostatecancer patient will experience a local or distant cancer recurrence.

INTRODUCTION

Prostate cancer is the most common solid malignancy in men and thesecond most common cause of cancer-related death in men in North Americaand the European Union (EU). In 2008, over 180,000 patients will bediagnosed with prostate cancer in the United States alone and nearly30,000 will die of this disease. Age is the single most important riskfactor for the development of prostate cancer, and applies across allracial groups that have been studied. With the aging of the U.S.population, it is projected that the annual incidence of prostate cancerwill double by 2025 to nearly 400,000 cases per year.

Since the introduction of prostate-specific antigen (PSA) screening inthe 1990's, the proportion of patients presenting with clinicallyevident disease has fallen dramatically such that patients categorizedas “low risk” now constitute half of new diagnoses today. PSA is used asa tumor marker to determine the presence of prostate cancer as high PSAlevels are associated with prostate cancer. Despite a growing proportionof localized prostate cancer patients presenting with low-risk featuressuch as low stage (T1) disease, greater than 90% of patients in the USstill undergo definitive therapy, including prostatectomy or radiation.Only about 15% of these patients would develop metastatic disease anddie from their prostate cancer, even in the absence of definitivetherapy. A. Bill-Axelson, et al., J Nat'l Cancer Inst. 100(16):1144-1154(2008). Therefore, the majority of prostate cancer patients are beingover-treated.

Estimates of recurrence risk and treatment decisions in prostate cancerare currently based primarily on PSA levels and/or tumor stage. Althoughtumor stage has been demonstrated to have significant association withoutcome sufficient to be included in pathology reports, the College ofAmerican Pathologists Consensus Statement noted that variations inapproach to the acquisition, interpretation, reporting, and analysis ofthis information exist. C. Compton, et al., Arch Pathol Lab Med124:979-992 (2000). As a consequence, existing pathologic stagingmethods have been criticized as lacking reproducibility and thereforemay provide imprecise estimates of individual patient risk.

SUMMARY

This application discloses molecular assays that involve measurement ofexpression level(s) of one or more genes, gene subsets, microRNAs, orone or more microRNAs in combination with one or more genes or genesubsets, from a biological sample obtained from a prostate cancerpatient, and analysis of the measured expression levels to provideinformation concerning the likelihood of cancer recurrence. For example,the likelihood of cancer recurrence could be described in terms of ascore based on clinical or biochemical recurrence-free interval.

In addition, this application discloses molecular assays that involvemeasurement of expression level(s) of one or more genes, gene subsets,microRNAs, or one or more microRNAs in combination with one or moregenes or gene subsets, from a biological sample obtained to identify arisk classification for a prostate cancer patient. For example, patientsmay be stratified using expression level(s) of one or more genes ormicroRNAs associated, positively or negatively, with cancer recurrenceor death from cancer, or with a prognostic factor. In an exemplaryembodiment, the prognostic factor is Gleason pattern.

The biological sample may be obtained from standard methods, includingsurgery, biopsy, or bodily fluids. It may comprise tumor tissue orcancer cells, and, in some cases, histologically normal tissue, e.g.,histologically normal tissue adjacent the tumor tissue. In exemplaryembodiments, the biological sample is positive or negative for a TMPRSS2fusion.

In exemplary embodiments, expression level(s) of one or more genesand/or microRNAs that are associated, positively or negatively, with aparticular clinical outcome in prostate cancer are used to determineprognosis and appropriate therapy. The genes disclosed herein may beused alone or arranged in functional gene subsets, such as celladhesion/migration, immediate-early stress response, and extracellularmatrix-associated. Each gene subset comprises the genes disclosedherein, as well as genes that are co-expressed with one or more of thedisclosed genes. The calculation may be performed on a computer,programmed to execute the gene expression analysis. The microRNAsdisclosed herein may also be used alone or in combination with any oneor more of the microRNAs and/or genes disclosed.

In exemplary embodiments, the molecular assay may involve expressionlevels for at least two genes. The genes, or gene subsets, may beweighted according to strength of association with prognosis or tumormicroenvironment. In another exemplary embodiment, the molecular assaymay involve expression levels of at least one gene and at least onemicroRNA. The gene-microRNA combination may be selected based on thelikelihood that the gene-microRNA combination functionally interact.

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1 shows the distribution of clinical and pathology assessments ofbiopsy Gleason score, baseline PSA level, and clinical T-stage.

DEFINITIONS

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Singleton et al., Dictionary ofMicrobiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York,N.Y. 1994), and March, Advanced Organic Chemistry Reactions, Mechanismsand Structure 4th ed., John Wiley & Sons (New York, N.Y. 1992), provideone skilled in the art with a general guide to many of the terms used inthe present application.

One skilled in the art will recognize many methods and materials similaror equivalent to those described herein, which could be used in thepractice of the present invention. Indeed, the present invention is inno way limited to the methods and materials described herein. Forpurposes of the invention, the following terms are defined below.

The terms “tumor” and “lesion” as used herein, refer to all neoplasticcell growth and proliferation, whether malignant or benign, and allpre-cancerous and cancerous cells and tissues. Those skilled in the artwill realize that a tumor tissue sample may comprise multiple biologicalelements, such as one or more cancer cells, partial or fragmented cells,tumors in various stages, surrounding histologically normal-appearingtissue, and/or macro or micro-dissected tissue.

The terms “cancer” and “cancerous” refer to or describe thephysiological condition in mammals that is typically characterized byunregulated cell growth. Examples of cancer in the present disclosureinclude cancer of the urogenital tract, such as prostate cancer.

The “pathology” of cancer includes all phenomena that compromise thewell-being of the patient. This includes, without limitation, abnormalor uncontrollable cell growth, metastasis, interference with the normalfunctioning of neighboring cells, release of cytokines or othersecretory products at abnormal levels, suppression or aggravation ofinflammatory or immunological response, neoplasia, premalignancy,malignancy, invasion of surrounding or distant tissues or organs, suchas lymph nodes, etc.

As used herein, the term “prostate cancer” is used interchangeably andin the broadest sense refers to all stages and all forms of cancerarising from the tissue of the prostate gland.

According to the tumor, node, metastasis (TNM) staging system of theAmerican Joint Committee on Cancer (AJCC), AJCC Cancer Staging Manual(7th Ed., 2010), the various stages of prostate cancer are defined asfollows: Tumor: T1: clinically inapparent tumor not palpable or visibleby imaging, T1a: tumor incidental histological finding in 5% or less oftissue resected, T1b: tumor incidental histological finding in more than5% of tissue resected, T1c: tumor identified by needle biopsy; T2: tumorconfined within prostate, T2a: tumor involves one half of one lobe orless, T2b: tumor involves more than half of one lobe, but not bothlobes, T2c: tumor involves both lobes; T3: tumor extends through theprostatic capsule, T3a: extracapsular extension (unilateral orbilateral), T3b: tumor invades seminal vesicle(s); T4: tumor is fixed orinvades adjacent structures other than seminal vesicles (bladder neck,external sphincter, rectum, levator muscles, or pelvic wall). Node: NO:no regional lymph node metastasis; N1: metastasis in regional lymphnodes. Metastasis: M0: no distant metastasis; M1: distant metastasispresent.

The Gleason Grading system is used to help evaluate the prognosis of menwith prostate cancer. Together with other parameters, it is incorporatedinto a strategy of prostate cancer staging, which predicts prognosis andhelps guide therapy. A Gleason “score” or “grade” is given to prostatecancer based upon its microscopic appearance. Tumors with a low Gleasonscore typically grow slowly enough that they may not pose a significantthreat to the patients in their lifetimes. These patients are monitored(“watchful waiting” or “active surveillance”) over time. Cancers with ahigher Gleason score are more aggressive and have a worse prognosis, andthese patients are generally treated with surgery (e.g., radicalprostectomy) and, in some cases, therapy (e.g., radiation, hormone,ultrasound, chemotherapy). Gleason scores (or sums) comprise grades ofthe two most common tumor patterns. These patterns are referred to asGleason patterns 1-5, with pattern 1 being the most well-differentiated.Most have a mixture of patterns. To obtain a Gleason score or grade, thedominant pattern is added to the second most prevalent pattern to obtaina number between 2 and 10. The Gleason Grades include: G1: welldifferentiated (slight anaplasia) (Gleason 2-4); G2: moderatelydifferentiated (moderate anaplasia) (Gleason 5-6); G3-4: poorlydifferentiated/undifferentiated (marked anaplasia) (Gleason 7-10).

Stage groupings: Stage I: T1a N0 M0 G1; Stage II: (T1a N0 M0 G2-4) or(T1b, c, T1, T2, N0 M0 Any G); Stage III: T3 N0 M0 Any G; Stage IV: (T4N0 M0 Any G) or (Any T N1 M0 Any G) or (Any T Any N M1 Any G).

As used herein, the term “tumor tissue” refers to a biological samplecontaining one or more cancer cells, or a fraction of one or more cancercells. Those skilled in the art will recognize that such biologicalsample may additionally comprise other biological components, such ashistologically appearing normal cells (e.g., adjacent the tumor),depending upon the method used to obtain the tumor tissue, such assurgical resection, biopsy, or bodily fluids.

As used herein, the term “AUA risk group” refers to the 2007 updatedAmerican Urological Association (AUA) guidelines for management ofclinically localized prostate cancer, which clinicians use to determinewhether a patient is at low, intermediate, or high risk of biochemical(PSA) relapse after local therapy.

As used herein, the term “adjacent tissue (AT)” refers to histologically“normal” cells that are adjacent a tumor. For example, the AT expressionprofile may be associated with disease recurrence and survival.

As used herein “non-tumor prostate tissue” refers to histologicallynormal-appearing tissue adjacent a prostate tumor.

Prognostic factors are those variables related to the natural history ofcancer, which influence the recurrence rates and outcome of patientsonce they have developed cancer. Clinical parameters that have beenassociated with a worse prognosis include, for example, increased tumorstage, PSA level at presentation, and Gleason grade or pattern.Prognostic factors are frequently used to categorize patients intosubgroups with different baseline relapse risks.

The term “prognosis” is used herein to refer to the likelihood that acancer patient will have a cancer-attributable death or progression,including recurrence, metastatic spread, and drug resistance, of aneoplastic disease, such as prostate cancer. For example, a “goodprognosis” would include long term survival without recurrence and a“bad prognosis” would include cancer recurrence.

As used herein, the term “expression level” as applied to a gene refersto the normalized level of a gene product, e.g. the normalized valuedetermined for the RNA expression level of a gene or for the polypeptideexpression level of a gene.

The term “gene product” or “expression product” are used herein to referto the RNA (ribonucleic acid) transcription products (transcripts) ofthe gene, including mRNA, and the polypeptide translation products ofsuch RNA transcripts. A gene product can be, for example, an unsplicedRNA, an mRNA, a splice variant mRNA, a microRNA, a fragmented RNA, apolypeptide, a post-translationally modified polypeptide, a splicevariant polypeptide, etc.

The term “RNA transcript” as used herein refers to the RNA transcriptionproducts of a gene, including, for example, mRNA, an unspliced RNA, asplice variant mRNA, a microRNA, and a fragmented RNA.

The term “microRNA” is used herein to refer to a small, non-coding,single-stranded RNA of ˜18-25 nucleotides that may regulate geneexpression. For example, when associated with the RNA-induced silencingcomplex (RISC), the complex binds to specific mRNA targets and causestranslation repression or cleavage of these mRNA sequences.

Unless indicated otherwise, each gene name used herein corresponds tothe Official Symbol assigned to the gene and provided by Entrez Gene(URL: www.ncbi.nlm.nih.gov/sites/entrez) as of the filing date of thisapplication.

The terms “correlated” and “associated” are used interchangeably hereinto refer to the association between two measurements (or measuredentities). The disclosure provides genes, gene subsets, microRNAs, ormicroRNAs in combination with genes or gene subsets, the expressionlevels of which are associated with tumor stage. For example, theincreased expression level of a gene or microRNA may be positivelycorrelated (positively associated) with a good or positive prognosis.Such a positive correlation may be demonstrated statistically in variousways, e.g. by a cancer recurrence hazard ratio less than one. In anotherexample, the increased expression level of a gene or microRNA may benegatively correlated (negatively associated) with a good or positiveprognosis. In that case, for example, the patient may experience acancer recurrence.

The terms “good prognosis” or “positive prognosis” as used herein referto a beneficial clinical outcome, such as long-term survival withoutrecurrence. The terms “bad prognosis” or “negative prognosis” as usedherein refer to a negative clinical outcome, such as cancer recurrence.

The term “risk classification” means a grouping of subjects by the levelof risk (or likelihood) that the subject will experience a particularclinical outcome. A subject may be classified into a risk group orclassified at a level of risk based on the methods of the presentdisclosure, e.g. high, medium, or low risk. A “risk group” is a group ofsubjects or individuals with a similar level of risk for a particularclinical outcome.

The term “long-term” survival is used herein to refer to survival for aparticular time period, e.g., for at least 5 years, or for at least 10years.

The term “recurrence” is used herein to refer to local or distantrecurrence (i.e., metastasis) of cancer. For example, prostate cancercan recur locally in the tissue next to the prostate or in the seminalvesicles. The cancer may also affect the surrounding lymph nodes in thepelvis or lymph nodes outside this area. Prostate cancer can also spreadto tissues next to the prostate, such as pelvic muscles, bones, or otherorgans. Recurrence can be determined by clinical recurrence detected by,for example, imaging study or biopsy, or biochemical recurrence detectedby, for example, sustained follow-up prostate-specific antigen (PSA)levels≥0.4 ng/mL or the initiation of salvage therapy as a result of arising PSA level.

The term “clinical recurrence-free interval (cRFI)” is used herein astime (in months) from surgery to first clinical recurrence or death dueto clinical recurrence of prostate cancer. Losses due to incompletefollow-up, other primary cancers or death prior to clinical recurrenceare considered censoring events; when these occur, the only informationknown is that up through the censoring time, clinical recurrence has notoccurred in this subject. Biochemical recurrences are ignored for thepurposes of calculating cRFI.

The term “biochemical recurrence-free interval (bRFI)” is used herein tomean the time (in months) from surgery to first biochemical recurrenceof prostate cancer. Clinical recurrences, losses due to incompletefollow-up, other primary cancers, or death prior to biochemicalrecurrence are considered censoring events.

The term “Overall Survival (OS)” is used herein to refer to the time (inmonths) from surgery to death from any cause. Losses due to incompletefollow-up are considered censoring events. Biochemical recurrence andclinical recurrence are ignored for the purposes of calculating OS.

The term “Prostate Cancer-Specific Survival (PCSS)” is used herein todescribe the time (in years) from surgery to death from prostate cancer.Losses due to incomplete follow-up or deaths from other causes areconsidered censoring events. Clinical recurrence and biochemicalrecurrence are ignored for the purposes of calculating PCSS.

The term “upgrading” or “upstaging” as used herein refers to a change inGleason grade from 3+3 at the time of biopsy to 3+4 or greater at thetime of radical prostatectomy (RP), or Gleason grade 3+4 at the time ofbiopsy to 4+3 or greater at the time of RP, or seminal vessicalinvolvement (SVI), or extracapsular involvement (ECE) at the time of RP.

In practice, the calculation of the measures listed above may vary fromstudy to study depending on the definition of events to be consideredcensored.

The term “microarray” refers to an ordered arrangement of hybridizablearray elements, e.g. oligonucleotide or polynucleotide probes, on asubstrate.

The term “polynucleotide” generally refers to any polyribonucleotide orpolydeoxribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA. Thus, for instance, polynucleotides as defined hereininclude, without limitation, single- and double-stranded DNA, DNAincluding single- and double-stranded regions, single- anddouble-stranded RNA, and RNA including single- and double-strandedregions, hybrid molecules comprising DNA and RNA that may besingle-stranded or, more typically, double-stranded or include single-and double-stranded regions. In addition, the term “polynucleotide” asused herein refers to triple-stranded regions comprising RNA or DNA orboth RNA and DNA. The strands in such regions may be from the samemolecule or from different molecules. The regions may include all of oneor more of the molecules, but more typically involve only a region ofsome of the molecules. One of the molecules of a triple-helical regionoften is an oligonucleotide. The term “polynucleotide” specificallyincludes cDNAs. The term includes DNAs (including cDNAs) and RNAs thatcontain one or more modified bases. Thus, DNAs or RNAs with backbonesmodified for stability or for other reasons, are “polynucleotides” asthat term is intended herein. Moreover, DNAs or RNAs comprising unusualbases, such as inosine, or modified bases, such as tritiated bases, areincluded within the term “polynucleotides” as defined herein. Ingeneral, the term “polynucleotide” embraces all chemically,enzymatically and/or metabolically modified forms of unmodifiedpolynucleotides, as well as the chemical forms of DNA and RNAcharacteristic of viruses and cells, including simple and complex cells.

The term “oligonucleotide” refers to a relatively short polynucleotide,including, without limitation, single-stranded deoxyribonucleotides,single- or double-stranded ribonucleotides, RNArDNA hybrids anddouble-stranded DNAs. Oligonucleotides, such as single-stranded DNAprobe oligonucleotides, are often synthesized by chemical methods, forexample using automated oligonucleotide synthesizers that arecommercially available. However, oligonucleotides can be made by avariety of other methods, including in vitro recombinant DNA-mediatedtechniques and by expression of DNAs in cells and organisms.

The term “Ct” as used herein refers to threshold cycle, the cycle numberin quantitative polymerase chain reaction (qPCR) at which thefluorescence generated within a reaction well exceeds the definedthreshold, i.e. the point during the reaction at which a sufficientnumber of amplicons have accumulated to meet the defined threshold.

The term “Cp” as used herein refers to “crossing point.” The Cp value iscalculated by determining the second derivatives of entire qPCRamplification curves and their maximum value. The Cp value representsthe cycle at which the increase of fluorescence is highest and where thelogarithmic phase of a PCR begins.

The terms “threshold” or “thresholding” refer to a procedure used toaccount for non-linear relationships between gene expressionmeasurements and clinical response as well as to further reducevariation in reported patient scores. When thresholding is applied, allmeasurements below or above a threshold are set to that threshold value.Non-linear relationship between gene expression and outcome could beexamined using smoothers or cubic splines to model gene expression inCox PH regression on recurrence free interval or logistic regression onrecurrence status. D. Cox, Journal of the Royal Statistical Society,Series B 34:187-220 (1972). Variation in reported patient scores couldbe examined as a function of variability in gene expression at the limitof quantitation and/or detection for a particular gene.

As used herein, the term “amplicon,” refers to pieces of DNA that havebeen synthesized using amplification techniques, such as polymerasechain reactions (PCR) and ligase chain reactions.

“Stringency” of hybridization reactions is readily determinable by oneof ordinary skill in the art, and generally is an empirical calculationdependent upon probe length, washing temperature, and saltconcentration. In general, longer probes require higher temperatures forproper annealing, while shorter probes need lower temperatures.Hybridization generally depends on the ability of denatured DNA tore-anneal when complementary strands are present in an environment belowtheir melting temperature. The higher the degree of desired homologybetween the probe and hybridizable sequence, the higher the relativetemperature which can be used. As a result, it follows that higherrelative temperatures would tend to make the reaction conditions morestringent, while lower temperatures less so. For additional details andexplanation of stringency of hybridization reactions, see Ausubel etal., Current Protocols in Molecular Biology (Wiley IntersciencePublishers, 1995).

“Stringent conditions” or “high stringency conditions”, as definedherein, typically: (1) employ low ionic strength and high temperaturefor washing, for example 0.015 M sodium chloride/0.0015 M sodiumcitrate/0.1% sodium dodecyl sulfate at 50° C.; (2) employ duringhybridization a denaturing agent, such as formamide, for example, 50%(v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1%polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with 750 mMsodium chloride, 75 mM sodium citrate at 42° C.; or (3) employ 50%formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodiumphosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt's solution,sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10% dextran sulfateat 42° C., with washes at 42° C. in 0.2×SSC (sodium chloride/sodiumcitrate) and 50% formamide, followed by a high-stringency washconsisting of 0.1×SSC containing EDTA at 55° C.

“Moderately stringent conditions” may be identified as described bySambrook et al., Molecular Cloning: A Laboratory Manual, New York: ColdSpring Harbor Press, 1989, and include the use of washing solution andhybridization conditions (e.g., temperature, ionic strength and % SDS)less stringent that those described above. An example of moderatelystringent conditions is overnight incubation at 37° C. in a solutioncomprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate),50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextransulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed bywashing the filters in 1×SSC at about 37-500 C. The skilled artisan willrecognize how to adjust the temperature, ionic strength, etc. asnecessary to accommodate factors such as probe length and the like.

The terms “splicing” and “RNA splicing” are used interchangeably andrefer to RNA processing that removes introns and joins exons to producemature mRNA with continuous coding sequence that moves into thecytoplasm of an eukaryotic cell.

The terms “co-express” and “co-expressed”, as used herein, refer to astatistical correlation between the amounts of different transcriptsequences across a population of different patients. Pairwiseco-expression may be calculated by various methods known in the art,e.g., by calculating Pearson correlation coefficients or Spearmancorrelation coefficients. Co-expressed gene cliques may also beidentified using graph theory. An analysis of co-expression may becalculated using normalized expression data. A gene is said to beco-expressed with a particular disclosed gene when the expression levelof the gene exhibits a Pearson correlation coefficient greater than orequal to 0.6.

A “computer-based system” refers to a system of hardware, software, anddata storage medium used to analyze information. The minimum hardware ofa patient computer-based system comprises a central processing unit(CPU), and hardware for data input, data output (e.g., display), anddata storage. An ordinarily skilled artisan can readily appreciate thatany currently available computer-based systems and/or components thereofare suitable for use in connection with the methods of the presentdisclosure. The data storage medium may comprise any manufacturecomprising a recording of the present information as described above, ora memory access device that can access such a manufacture.

To “record” data, programming or other information on a computerreadable medium refers to a process for storing information, using anysuch methods as known in the art. Any convenient data storage structuremay be chosen, based on the means used to access the stored information.A variety of data processor programs and formats can be used forstorage, e.g. word processing text file, database format, etc.

A “processor” or “computing means” references any hardware and/orsoftware combination that will perform the functions required of it. Forexample, a suitable processor may be a programmable digitalmicroprocessor such as available in the form of an electroniccontroller, mainframe, server or personal computer (desktop orportable). Where the processor is programmable, suitable programming canbe communicated from a remote location to the processor, or previouslysaved in a computer program product (such as a portable or fixedcomputer readable storage medium, whether magnetic, optical or solidstate device based). For example, a magnetic medium or optical disk maycarry the programming, and can be read by a suitable readercommunicating with each processor at its corresponding station.

As used herein, the terms “active surveillance” and “watchful waiting”mean closely monitoring a patient's condition without giving anytreatment until symptoms appear or change. For example, in prostatecancer, watchful waiting is usually used in older men with other medicalproblems and early-stage disease.

As used herein, the term “surgery” applies to surgical methodsundertaken for removal of cancerous tissue, including pelviclymphadenectomy, radical prostatectomy, transurethral resection of theprostate (TURP), excision, dissection, and tumor biopsy/removal. Thetumor tissue or sections used for gene expression analysis may have beenobtained from any of these methods.

As used herein, the term “therapy” includes radiation, hormonal therapy,cryosurgery, chemotherapy, biologic therapy, and high-intensity focusedultrasound.

As used herein, the term “TMPRSS fusion” and “TMPRSS2 fusion” are usedinterchangeably and refer to a fusion of the androgen-driven TMPRSS2gene with the ERG oncogene, which has been demonstrated to have asignificant association with prostate cancer. S. Perner, et al., UrologeA. 46(7):754-760 (2007); S. A. Narod, et al., Br J Cancer 99(6):847-851(2008). As used herein, positive TMPRSS fusion status indicates that theTMPRSS fusion is present in a tissue sample, whereas negative TMPRSSfusion status indicates that the TMPRSS fusion is not present in atissue sample. Experts skilled in the art will recognize that there arenumerous ways to determine TMPRSS fusion status, such as real-time,quantitative PCR or high-throughput sequencing. See, e.g., K. Mertz, etal., Neoplasis 9(3):200-206 (2007); C. Maher, Nature 458(7234):97-101(2009).

Gene Expression Methods Using Genes, Gene Subsets, and MicroRNAs

The present disclosure provides molecular assays that involvemeasurement of expression level(s) of one or more genes, gene subsets,microRNAs, or one or more microRNAs in combination with one or moregenes or gene subsets, from a biological sample obtained from a prostatecancer patient, and analysis of the measured expression levels toprovide information concerning the likelihood of cancer recurrence.

The present disclosure further provides methods to classify a prostatetumor based on expression level(s) of one or more genes and/ormicroRNAs. The disclosure further provides genes and/or microRNAs thatare associated, positively or negatively, with a particular prognosticoutcome. In exemplary embodiments, the clinical outcomes include cRFIand bRFI. In another embodiment, patients may be classified in riskgroups based on the expression level(s) of one or more genes and/ormicroRNAs that are associated, positively or negatively, with aprognostic factor. In an exemplary embodiment, that prognostic factor isGleason pattern.

Various technological approaches for determination of expression levelsof the disclosed genes and microRNAs are set forth in thisspecification, including, without limitation, RT-PCR, microarrays,high-throughput sequencing, serial analysis of gene expression (SAGE)and Digital Gene Expression (DGE), which will be discussed in detailbelow. In particular aspects, the expression level of each gene ormicroRNA may be determined in relation to various features of theexpression products of the gene including exons, introns, proteinepitopes and protein activity.

The expression level(s) of one or more genes and/or microRNAs may bemeasured in tumor tissue. For example, the tumor tissue may obtainedupon surgical removal or resection of the tumor, or by tumor biopsy. Thetumor tissue may be or include histologically “normal” tissue, forexample histologically “normal” tissue adjacent to a tumor. Theexpression level of genes and/or microRNAs may also be measured in tumorcells recovered from sites distant from the tumor, for examplecirculating tumor cells, body fluid (e.g., urine, blood, blood fraction,etc.).

The expression product that is assayed can be, for example, RNA or apolypeptide. The expression product may be fragmented. For example, theassay may use primers that are complementary to target sequences of anexpression product and could thus measure full transcripts as well asthose fragmented expression products containing the target sequence.Further information is provided in Table A (inserted in specificationprior to claims).

The RNA expression product may be assayed directly or by detection of acDNA product resulting from a PCR-based amplification method, e.g.,quantitative reverse transcription polymerase chain reaction (qRT-PCR).(See e.g., U.S. Pat. No. 7,587,279). Polypeptide expression product maybe assayed using immunohistochemistry (IHC). Further, both RNA andpolypeptide expression products may also be is assayed usingmicroarrays.

Clinical Utility

Prostate cancer is currently diagnosed using a digital rectal exam (DRE)and Prostate-specific antigen (PSA) test. If PSA results are high,patients will generally undergo a prostate tissue biopsy. Thepathologist will review the biopsy samples to check for cancer cells anddetermine a Gleason score. Based on the Gleason score, PSA, clinicalstage, and other factors, the physician must make a decision whether tomonitor the patient, or treat the patient with surgery and therapy.

At present, clinical decision-making in early stage prostate cancer isgoverned by certain histopathologic and clinical factors. These include:(1) tumor factors, such as clinical stage (e.g. T1, T2), PSA level atpresentation, and Gleason grade, that are very strong prognostic factorsin determining outcome; and (2) host factors, such as age at diagnosisand co-morbidity. Because of these factors, the most clinically usefulmeans of stratifying patients with localized disease according toprognosis has been through multifactorial staging, using the clinicalstage, the serum PSA level, and tumor grade (Gleason grade) together. Inthe 2007 updated American Urological Association (AUA) guidelines formanagement of clinically localized prostate cancer, these parametershave been grouped to determine whether a patient is at low,intermediate, or high risk of biochemical (PSA) relapse after localtherapy. I. Thompson, et al., Guideline for the management of clinicallylocalized prostate cancer, J Urol. 177(6):2106-31 (2007).

Although such classifications have proven to be helpful indistinguishing patients with localized disease who may need adjuvanttherapy after surgery/radiation, they have less ability to discriminatebetween indolent cancers, which do not need to be treated with localtherapy, and aggressive tumors, which require local therapy. In fact,these algorithms are of increasingly limited use for deciding betweenconservative management and definitive therapy because the bulk ofprostate cancers diagnosed in the PSA screening era now present withclinical stage T1c and PSA≤10 ng/mL.

Patients with T1 prostate cancer have disease that is not clinicallyapparent but is discovered either at transurethral resection of theprostate (TURP, T1a, T1b) or at biopsy performed because of an elevatedPSA (>4 ng/mL, T1c). Approximately 80% of the cases presenting in 2007are clinical T1 at diagnosis. In a Scandinavian trial, OS at 10 yearswas 85% for patients with early stage prostate cancer (T1/T2) andGleason score≤7, after radical prostatectomy.

Patients with T2 prostate cancer have disease that is clinically evidentand is organ confined; patients with T3 tumors have disease that haspenetrated the prostatic capsule and/or has invaded the seminalvesicles. It is known from surgical series that clinical stagingunderestimates pathological stage, so that about 20% of patients who areclinically T2 will be pT3 after prostatectomy. Most of patients with T2or T3 prostate cancer are treated with local therapy, eitherprostatectomy or radiation. The data from the Scandinavian trial suggestthat for T2 patients with Gleason grade≤7, the effect of prostatectomyon survival is at most 5% at 10 years; the majority of patients do notbenefit from surgical treatment at the time of diagnosis. For T2patients with Gleason≥7 or for T3 patients, the treatment effect ofprostatectomy is assumed to be significant but has not been determinedin randomized trials. It is known that these patients have a significantrisk (10-30%) of recurrence at 10 years after local treatment, however,there are no prospective randomized trials that define the optimal localtreatment (radical prostatectomy, radiation) at diagnosis, whichpatients are likely to benefit from neo-adjuvant/adjuvant androgendeprivation therapy, and whether treatment (androgen deprivation,chemotherapy) at the time of biochemical failure (elevated PSA) has anyclinical benefit.

Accurately determining Gleason scores from needle biopsies presentsseveral technical challenges. First, interpreting histology that is“borderline” between Gleason pattern is highly subjective, even forurologic pathologists. Second, incomplete biopsy sampling is yet anotherreason why the “predicted” Gleason score on biopsy does not alwayscorrelate with the actual “observed” Gleason score of the prostatecancer in the gland itself. Hence, the accuracy of Gleason scoring isdependent upon not only the expertise of the pathologist reading theslides, but also on the completeness and adequacy of the prostate biopsysampling strategy. T. Stamey, Urology 45:2-12 (1995). The gene/microRNAexpression assay and associated information provided by the practice ofthe methods disclosed herein provide a molecular assay method tofacilitate optimal treatment decision-making in early stage prostatecancer. An exemplary embodiment provides genes and microRNAs, theexpression levels of which are associated (positively or negatively)with prostate cancer recurrence. For example, such a clinical tool wouldenable physicians to identify T2/T3 patients who are likely to recurfollowing definitive therapy and need adjuvant treatment.

In addition, the methods disclosed herein may allow physicians toclassify tumors, at a molecular level, based on expression level(s) ofone or more genes and/or microRNAs that are significantly associatedwith prognostic factors, such as Gleason pattern and TMPRSS fusionstatus. These methods would not be impacted by the technicaldifficulties of intra-patient variability, histologically determiningGleason pattern in biopsy samples, or inclusion of histologically normalappearing tissue adjacent to tumor tissue. Multi-analyte gene/microRNAexpression tests can be used to measure the expression level of one ormore genes and/or microRNAs involved in each of several relevantphysiologic processes or component cellular characteristics. The methodsdisclosed herein may group the genes and/or microRNAs. The grouping ofgenes and microRNAs may be performed at least in part based on knowledgeof the contribution of those genes and/or microRNAs according tophysiologic functions or component cellular characteristics, such as inthe groups discussed above. Furthermore, one or more microRNAs may becombined with one or moregenes. The gene-microRNA combination may beselected based on the likelihood that the gene-microRNA combinationfunctionally interact. The formation of groups (or gene subsets), inaddition, can facilitate the mathematical weighting of the contributionof various expression levels to cancer recurrence. The weighting of agene/microRNA group representing a physiological process or componentcellular characteristic can reflect the contribution of that process orcharacteristic to the pathology of the cancer and clinical outcome.

Optionally, the methods disclosed may be used to classify patients byrisk, for example risk of recurrence. Patients can be partitioned intosubgroups (e.g., tertiles or quartiles) and the values chosen willdefine subgroups of patients with respectively greater or lesser risk.

The utility of a disclosed gene marker in predicting prognosis may notbe unique to that marker. An alternative marker having an expressionpattern that is parallel to that of a disclosed gene may be substitutedfor, or used in addition to, that co-expressed gene or microRNA. Due tothe co-expression of such genes or microRNAs, substitution of expressionlevel values should have little impact on the overall utility of thetest. The closely similar expression patterns of two genes or microRNAsmay result from involvement of both genes or microRNAs in the sameprocess and/or being under common regulatory control in prostate tumorcells. The present disclosure thus contemplates the use of suchco-expressed genes, gene subsets, or microRNAs as substitutes for, or inaddition to, genes of the present disclosure.

Methods of Assaying Expression Levels of a Gene Product

The methods and compositions of the present disclosure will employ,unless otherwise indicated, conventional techniques of molecular biology(including recombinant techniques), microbiology, cell biology, andbiochemistry, which are within the skill of the art. Exemplarytechniques are explained fully in the literature, such as, “MolecularCloning: A Laboratory Manual”, 2nd edition (Sambrook et al., 1989);“Oligonucleotide Synthesis” (M. J. Gait, ed., 1984); “Animal CellCulture” (R. I. Freshney, ed., 1987); “Methods in Enzymology” (AcademicPress, Inc.); “Handbook of Experimental Immunology”, 4th edition (D. M.Weir & C. C. Blackwell, eds., Blackwell Science Inc., 1987); “GeneTransfer Vectors for Mammalian Cells” (J. M. Miller & M. P. Calos, eds.,1987); “Current Protocols in Molecular Biology” (F. M. Ausubel et al.,eds., 1987); and “PCR: The Polymerase Chain Reaction”, (Mullis et al.,eds., 1994).

Methods of gene expression profiling include methods based onhybridization analysis of polynucleotides, methods based on sequencingof polynucleotides, and proteomics-based methods. Exemplary methodsknown in the art for the quantification of RNA expression in a sampleinclude northern blotting and in situ hybridization (Parker & Barnes,Methods in Molecular Biology 106:247-283 (1999)); RNAse protectionassays (Hod, Biotechniques 13:852-854 (1992)); and PCR-based methods,such as reverse transcription PCT (RT-PCR) (Weis et al., Trends inGenetics 8:263-264 (1992)). Antibodies may be employed that canrecognize sequence-specific duplexes, including DNA duplexes, RNAduplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes.Representative methods for sequencing-based gene expression analysisinclude Serial Analysis of Gene Expression (SAGE), and gene expressionanalysis by massively parallel signature sequencing (MPSS).

Reverse Transcriptase PCR (RT-PCR)

Typically, mRNA or microRNA is isolated from a test sample. The startingmaterial is typically total RNA isolated from a human tumor, usuallyfrom a primary tumor. Optionally, normal tissues from the same patientcan be used as an internal control. Such normal tissue can behistologically-appearing normal tissue adjacent a tumor. mRNA ormicroRNA can be extracted from a tissue sample, e.g., from a sample thatis fresh, frozen (e.g. fresh frozen), or paraffin-embedded and fixed(e.g. formalin-fixed).

General methods for mRNA and microRNA extraction are well known in theart and are disclosed in standard textbooks of molecular biology,including Ausubel et al., Current Protocols of Molecular Biology, JohnWiley and Sons (1997). Methods for RNA extraction from paraffin embeddedtissues are disclosed, for example, in Rupp and Locker, Lab Invest.56:A67 (1987), and De Andrés et al., BioTechniques 18:42044 (1995). Inparticular, RNA isolation can be performed using a purification kit,buffer set and protease from commercial manufacturers, such as Qiagen,according to the manufacturer's instructions. For example, total RNAfrom cells in culture can be isolated using Qiagen RNeasy mini-columns.Other commercially available RNA isolation kits include MasterPure™Complete DNA and RNA Purification Kit (EPICENTRE®, Madison, Wis.), andParaffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissuesamples can be isolated using RNA Stat-60 (Tel-Test). RNA prepared fromtumor can be isolated, for example, by cesium chloride density gradientcentrifugation.

The sample containing the RNA is then subjected to reverse transcriptionto produce cDNA from the RNA template, followed by exponentialamplification in a PCR reaction. The two most commonly used reversetranscriptases are avilo myeloblastosis virus reverse transcriptase(AMV-RT) and Moloney murine leukemia virus reverse transcriptase(MMLV-RT). The reverse transcription step is typically primed usingspecific primers, random hexamers, or oligo-dT primers, depending on thecircumstances and the goal of expression profiling. For example,extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit(Perkin Elmer, Calif., USA), following the manufacturer's instructions.The derived cDNA can then be used as a template in the subsequent PCRreaction.

PCR-based methods use a thermostable DNA-dependent DNA polymerase, suchas a Taq DNA polymerase. For example, TaqMan® PCR typically utilizes the5′-nuclease activity of Taq or Tth polymerase to hydrolyze ahybridization probe bound to its target amplicon, but any enzyme withequivalent 5′ nuclease activity can be used. Two oligonucleotide primersare used to generate an amplicon typical of a PCR reaction product. Athird oligonucleotide, or probe, can be designed to facilitate detectionof a nucleotide sequence of the amplicon located between thehybridization sites the two PCR primers. The probe can be detectablylabeled, e.g., with a reporter dye, and can further be provided withboth a fluorescent dye, and a quencher fluorescent dye, as in a Taqman®probe configuration. Where a Taqman® probe is used, during theamplification reaction, the Taq DNA polymerase enzyme cleaves the probein a template-dependent manner. The resultant probe fragmentsdisassociate in solution, and signal from the released reporter dye isfree from the quenching effect of the second fluorophore. One moleculeof reporter dye is liberated for each new molecule synthesized, anddetection of the unquenched reporter dye provides the basis forquantitative interpretation of the data.

TaqMan® RT-PCR can be performed using commercially available equipment,such as, for example, high-throughput platforms such as the ABI PRISM7700 Sequence Detection System® (Perkin-Elmer-Applied Biosystems, FosterCity, Calif., USA), or Lightcycler (Roche Molecular Biochemicals,Mannheim, Germany). In a preferred embodiment, the procedure is run on aLightCycler® 480 (Roche Diagnostics) real-time PCR system, which is amicrowell plate-based cycler platform.

5′-Nuclease assay data are commonly initially expressed as a thresholdcycle (“CT”). Fluorescence values are recorded during every cycle andrepresent the amount of product amplified to that point in theamplification reaction. The threshold cycle (CT) is generally describedas the point when the fluorescent signal is first recorded asstatistically significant. Alternatively, data may be expressed as acrossing point (“Cp”). The Cp value is calculated by determining thesecond derivatives of entire qPCR amplification curves and their maximumvalue. The Cp value represents the cycle at which the increase offluorescence is highest and where the logarithmic phase of a PCR begins.

To minimize errors and the effect of sample-to-sample variation, RT-PCRis usually performed using an internal standard. The ideal internalstandard gene (also referred to as a reference gene) is expressed at aquite constant level among cancerous and non-cancerous tissue of thesame origin (i.e., a level that is not significantly different amongnormal and cancerous tissues), and is not significantly affected by theexperimental treatment (i.e., does not exhibit a significant differencein expression level in the relevant tissue as a result of exposure tochemotherapy), and expressed at a quite constant level among the sametissue taken from different patients. For example, reference genesuseful in the methods disclosed herein should not exhibit significantlydifferent expression levels in cancerous prostate as compared to normalprostate tissue. RNAs frequently used to normalize patterns of geneexpression are mRNAs for the housekeeping genesglyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and β-actin. Exemplaryreference genes used for normalization comprise one or more of thefollowing genes: AAMP, ARF1, ATP5E, CLTC, GPS1, and PGK1. Geneexpression measurements can be normalized relative to the mean of one ormore (e.g., 2, 3, 4, 5, or more) reference genes. Reference-normalizedexpression measurements can range from 2 to 15, where a one unitincrease generally reflects a 2-fold increase in RNA quantity.

Real time PCR is compatible both with quantitative competitive PCR,where internal competitor for each target sequence is used fornormalization, and with quantitative comparative PCR using anormalization gene contained within the sample, or a housekeeping genefor RT-PCR. For further details see, e.g. Held et al., Genome Research6:986-994 (1996).

The steps of a representative protocol for use in the methods of thepresent disclosure use fixed, paraffin-embedded tissues as the RNAsource. For example, mRNA isolation, purification, primer extension andamplification can be performed according to methods available in theart. (see, e.g., Godfrey et al. J. Molec. Diagnostics 2: 84-91 (2000);Specht et al., Am. J. Pathol. 158: 419-29 (2001)). Briefly, arepresentative process starts with cutting about 10 μm thick sections ofparaffin-embedded tumor tissue samples. The RNA is then extracted, andprotein and DNA depleted from the RNA-containing sample. After analysisof the RNA concentration, RNA is reverse transcribed using gene specificprimers followed by RT-PCR to provide for cDNA amplification products.

Design of Intron-Based PCR Primers and Probes

PCR primers and probes can be designed based upon exon or intronsequences present in the mRNA transcript of the gene of interest.Primer/probe design can be performed using publicly available software,such as the DNA BLAT software developed by Kent, W. J., Genome Res.12(4):656-64 (2002), or by the BLAST software including its variations.

Where necessary or desired, repetitive sequences of the target sequencecan be masked to mitigate non-specific signals. Exemplary tools toaccomplish this include the Repeat Masker program available on-linethrough the Baylor College of Medicine, which screens DNA sequencesagainst a library of repetitive elements and returns a query sequence inwhich the repetitive elements are masked. The masked intron sequencescan then be used to design primer and probe sequences using anycommercially or otherwise publicly available primer/probe designpackages, such as Primer Express (Applied Biosystems); MGBassay-by-design (Applied Biosystems); Primer3 (Steve Rozen and Helen J.Skaletsky (2000) Primer3 on the WWW for general users and for biologistprogrammers. See S. Rrawetz, S. Misener, Bioinformatics Methods andProtocols: Methods in Molecular Biology, pp. 365-386 (Humana Press).

Other factors that can influence PCR primer design include primerlength, melting temperature (Tm), and G/C content, specificity,complementary primer sequences, and 3′-end sequence. In general, optimalPCR primers are generally 17-30 bases in length, and contain about20-80%, such as, for example, about 50-60% G+C bases, and exhibit Tm'sbetween 50 and 80 OC, e.g. about 50 to 70° C.

For further guidelines for PCR primer and probe design see, e.g.Dieffenbach, C W. et al, “General Concepts for PCR Primer Design” in:PCR Primer, A Laboratory Manual, Cold Spring Harbor Laboratory Press.New York, 1995, pp. 133-155; Innis and Gelfand, “Optimization of PCRs”in: PCR Protocols, A Guide to Methods and Applications, CRC Press,London, 1994, pp. 5-11; and Plasterer, T. N. Primerselect: Primer andprobe design. Methods Mol. Biol. 70:520-527 (1997), the entiredisclosures of which are hereby expressly incorporated by reference.

Table A provides further information concerning the primer, probe, andamplicon sequences associated with the Examples disclosed herein.

MassARRAY® System

In MassARRAY-based methods, such as the exemplary method developed bySequenom, Inc. (San Diego, Calif.) following the isolation of RNA andreverse transcription, the obtained cDNA is spiked with a synthetic DNAmolecule (competitor), which matches the targeted cDNA region in allpositions, except a single base, and serves as an internal standard. ThecDNA/competitor mixture is PCR amplified and is subjected to a post-PCRshrimp alkaline phosphatase (SAP) enzyme treatment, which results in thedephosphorylation of the remaining nucleotides. After inactivarion ofthe alkaline phosphatase, the PCR products from the competitor and cDNAare subjected to primer extension, which generates distinct mass signalsfor the competitor- and cDNA-derives PCR products. After purification,these products are dispensed on a chip array, which is pre-loaded withcomponents needed for analysis with matrix-assisted laser desorptionionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. ThecDNA present in the reaction is then quantified by analyzing the ratiosof the peak areas in the mass spectrum generated. For further detailssee, e.g. Ding and Cantor, Proc. Natl. Acad. Sci. USA 100:3059-3064(2003).

Other PCR-Based Methods

Further PCR-based techniques that can find use in the methods disclosedherein include, for example, BeadArray® technology (Illumina, San Diego,Calif.; Oliphant et al., Discovery of Markers for Disease (Supplement toBiotechniques), June 2002; Ferguson et al., Analytical Chemistry 72:5618(2000)); BeadsArray for Detection of Gene Expression® (BADGE), using thecommercially available LuminexlOO LabMAP® system and multiplecolor-coded microspheres (Luminex Corp., Austin, Tex.) in a rapid assayfor gene expression (Yang et al., Genome Res. 11:1888-1898 (2001)); andhigh coverage expression profiling (HiCEP) analysis (Fukumura et al.,Nucl. Acids. Res. 31(16) e94 (2003).

Microarrays

Expression levels of a gene or microArray of interest can also beassessed using the microarray technique. In this method, polynucleotidesequences of interest (including cDNAs and oligonucleotides) are arrayedon a substrate. The arrayed sequences are then contacted underconditions suitable for specific hybridization with detectably labeledcDNA generated from RNA of a test sample. As in the RT-PCR method, thesource of RNA typically is total RNA isolated from a tumor sample, andoptionally from normal tissue of the same patient as an internal controlor cell lines. RNA can be extracted, for example, from frozen orarchived paraffin-embedded and fixed (e.g. formalin-fixed) tissuesamples.

For example, PCR amplified inserts of cDNA clones of a gene to beassayed are applied to a substrate in a dense array. Usually at least10,000 nucleotide sequences are applied to the substrate. For example,the microarrayed genes, immobilized on the microchip at 10,000 elementseach, are suitable for hybridization under stringent conditions.Fluorescently labeled cDNA probes may be generated through incorporationof fluorescent nucleotides by reverse transcription of RNA extractedfrom tissues of interest. Labeled cDNA probes applied to the chiphybridize with specificity to each spot of DNA on the array. Afterwashing under stringent conditions to remove non-specifically boundprobes, the chip is scanned by confocal laser microscopy or by anotherdetection method, such as a CCD camera. Quantitation of hybridization ofeach arrayed element allows for assessment of corresponding RNAabundance.

With dual color fluorescence, separately labeled cDNA probes generatedfrom two sources of RNA are hybridized pair wise to the array. Therelative abundance of the transcripts from the two sources correspondingto each specified gene is thus determined simultaneously. Theminiaturized scale of the hybridization affords a convenient and rapidevaluation of the expression pattern for large numbers of genes. Suchmethods have been shown to have the sensitivity required to detect raretranscripts, which are expressed at a few copies per cell, and toreproducibly detect at least approximately two-fold differences in theexpression levels (Schena et at, Proc. Natl. Acad. ScL USA 93(2):106-149(1996)). Microarray analysis can be performed by commercially availableequipment, following manufacturer's protocols, such as by using theAffymetrix GenChip® technology, or Incyte's microarray technology.

Serial Analysis of Gene Expression (SAGE)

Serial analysis of gene expression (SAGE) is a method that allows thesimultaneous and quantitative analysis of a large number of genetranscripts, without the need of providing an individual hybridizationprobe for each transcript. First, a short sequence tag (about 10-14 bp)is generated that contains sufficient information to uniquely identify atranscript, provided that the tag is obtained from a unique positionwithin each transcript. Then, many transcripts are linked together toform long serial molecules, that can be sequenced, revealing theidentity of the multiple tags simultaneously. The expression pattern ofany population of transcripts can be quantitatively evaluated bydetermining the abundance of individual tags, and identifying the genecorresponding to each tag. For more details see, e.g. Velculescu et al.,Science 270:484-487 (1995); and Velculescu et al., Cell 88:243-51(1997).

Gene Expression Analysis by Nucleic Acid Sequencing

Nucleic acid sequencing technologies are suitable methods for analysisof gene expression. The principle underlying these methods is that thenumber of times a cDNA sequence is detected in a sample is directlyrelated to the relative expression of the RNA corresponding to thatsequence. These methods are sometimes referred to by the term DigitalGene Expression (DGE) to reflect the discrete numeric property of theresulting data. Early methods applying this principle were SerialAnalysis of Gene Expression (SAGE) and Massively Parallel SignatureSequencing (MPSS). See, e.g., S. Brenner, et al., Nature Biotechnology18(6):630-634 (2000). More recently, the advent of “next-generation”sequencing technologies has made DGE simpler, higher throughput, andmore affordable. As a result, more laboratories are able to utilize DGEto screen the expression of more genes in more individual patientsamples than previously possible. See, e.g., J. Marioni, Genome Research18(9):1509-1517 (2008); R. Morin, Genome Research 18(4):610-621 (2008);A. Mortazavi, Nature Methods 5(7):621-628 (2008); N. Cloonan, NatureMethods 5(7):613-619 (2008).

Isolating RNA from Body Fluids

Methods of isolating RNA for expression analysis from blood, plasma andserum (see, e.g., K. Enders, et al., Clin Chem 48, 1647-53 (2002) (andreferences cited therein) and from urine (see, e.g., R. Boom, et al., JClin Microbiol. 28, 495-503 (1990) and references cited therein) havebeen described.

Immunohistochemistry

Immunohistochemistry methods are also suitable for detecting theexpression levels of genes and applied to the method disclosed herein.Antibodies (e.g., monoclonal antibodies) that specifically bind a geneproduct of a gene of interest can be used in such methods. Theantibodies can be detected by direct labeling of the antibodiesthemselves, for example, with radioactive labels, fluorescent labels,hapten' labels such as, biotin, or an enzyme such as horse radishperoxidase or alkaline phosphatase. Alternatively, unlabeled primaryantibody can be used in conjunction with a labeled secondary antibodyspecific for the primary antibody. Immunohistochemistry protocols andkits are well known in the art and are commercially available.

Proteomics

The term “proteome” is defined as the totality of the proteins presentin a sample (e.g. tissue, organism, or cell culture) at a certain pointof time. Proteomics includes, among other things, study of the globalchanges of protein expression in a sample (also referred to as“expression proteomics”). Proteomics typically includes the followingsteps: (1) separation of individual proteins in a sample by 2-D gelelectrophoresis (2-D PAGE); (2) identification of the individualproteins recovered from the gel, e.g. my mass spectrometry or N-terminalsequencing, and (3) analysis of the data using bioinformatics.

General Description of the mRNA/microRNA Isolation, Purification andAmplification

The steps of a representative protocol for profiling gene expressionusing fixed, paraffin-embedded tissues as the RNA source, including mRNAor microRNA isolation, purification, primer extension and amplificationare provided in various published journal articles. (See, e.g., T. E.Godfrey, et al. J. Molec. Diagnostics 2: 84-91 (2000); K. Specht et al.,Am. J. Pathol. 158: 419-29 (2001), M. Cronin, et al., Am J Pathol164:35-42 (2004)). Briefly, a representative process starts with cuttinga tissue sample section (e.g. about 10 μm thick sections of aparaffin-embedded tumor tissue sample). The RNA is then extracted, andprotein and DNA are removed. After analysis of the RNA concentration,RNA repair is performed if desired. The sample can then be subjected toanalysis, e.g., by reverse transcribed using gene specific promotersfollowed by RT-PCR.

Statistical Analysis of Expression Levels in Identification of Genes andMicroRNAs

One skilled in the art will recognize that there are many statisticalmethods that may be used to determine whether there is a significantrelationship between a parameter of interest (e.g., recurrence) andexpression levels of a marker gene/microRNA as described here. In anexemplary embodiment, the present invention provides a stratified cohortsampling design (a form of case-control sampling) using tissue and datafrom prostate cancer patients. Selection of specimens was stratified byT stage (T1, T2), year cohort (<1993, ≥1993), and prostatectomy GleasonScore (low/intermediate, high). All patients with clinical recurrencewere selected and a sample of patients who did not experience a clinicalrecurrence was selected. For each patient, up to two enriched tumorspecimens and one normal-appearing tissue sample was assayed.

All hypothesis tests were reported using two-sided p-values. Toinvestigate if there is a significant relationship of outcomes (clinicalrecurrence-free interval (cRFI), biochemical recurrence-free interval(bRFI), prostate cancer-specific survival (PCSS), and overall survival(OS)) with individual genes and/or microRNAs, demographic or clinicalcovariates Cox Proportional Hazards (PH) models using maximum weightedpseudo partial-likelihood estimators were used and p-values from Waldtests of the null hypothesis that the hazard ratio (HR) is one arereported. To investigate if there is a significant relationship betweenindividual genes and/or microRNAs and Gleason pattern of a particularsample, ordinal logistic regression models using maximum weightedlikelihood methods were used and p-values from Wald tests of the nullhypothesis that the odds ratio (OR) is one are reported.

Coexpression Analysis

The present disclosure provides a method to determine tumor stage basedon the expression of staging genes, or genes that co-express withparticular staging genes. To perform particular biological processes,genes often work together in a concerted way, i.e. they areco-expressed. Co-expressed gene groups identified for a disease processlike cancer can serve as biomarkers for tumor status and diseaseprogression. Such co-expressed genes can be assayed in lieu of, or inaddition to, assaying of the staging gene with which they areco-expressed.

In an exemplary embodiment, the joint correlation of gene expressionlevels among prostate cancer specimens under study may be assessed. Forthis purpose, the correlation structures among genes and specimens maybe examined through hierarchical cluster methods. This information maybe used to confirm that genes that are known to be highly correlated inprostate cancer specimens cluster together as expected. Only genesexhibiting a nominally significant (unadjusted p<0.05) relationship withcRFI in the univariate Cox PH regression analysis will be included inthese analyses.

One skilled in the art will recognize that many co-expression analysismethods now known or later developed will fall within the scope andspirit of the present invention. These methods may incorporate, forexample, correlation coefficients, co-expression network analysis,clique analysis, etc., and may be based on expression data from RT-PCR,microarrays, sequencing, and other similar technologies. For example,gene expression clusters can be identified using pair-wise analysis ofcorrelation based on Pearson or Spearman correlation coefficients. (See,e.g., Pearson K. and Lee A., Biometrika 2, 357 (1902); C. Spearman,Amer. J. Psychol 15:72-101 (1904); J. Myers, A. Well, Research Designand Statistical Analysis, p. 508 (2nd Ed., 2003).)

Normalization of Expression Levels

The expression data used in the methods disclosed herein can benormalized. Normalization refers to a process to correct for (normalizeaway), for example, differences in the amount of RNA assayed andvariability in the quality of the RNA used, to remove unwanted sourcesof systematic variation in Ct or Cp measurements, and the like. Withrespect to RT-PCR experiments involving archived fixed paraffin embeddedtissue samples, sources of systematic variation are known to include thedegree of RNA degradation relative to the age of the patient sample andthe type of fixative used to store the sample. Other sources ofsystematic variation are attributable to laboratory processingconditions.

Assays can provide for normalization by incorporating the expression ofcertain normalizing genes, which do not significantly differ inexpression levels under the relevant conditions. Exemplary normalizationgenes disclosed herein include housekeeping genes. (See, e.g., E.Eisenberg, et al., Trends in Genetics 19(7):362-365 (2003).)Normalization can be based on the mean or median signal (Ct or Cp) ofall of the assayed genes or a large subset thereof (global normalizationapproach). In general, the normalizing genes, also referred to asreference genes should be genes that are known not to exhibitsignificantly different expression in prostate cancer as compared tonon-cancerous prostate tissue, and are not significantly affected byvarious sample and process conditions, thus provide for normalizing awayextraneous effects.

In exemplary embodiments, one or more of the following genes are used asreferences by which the mRNA or microRNA expression data is normalized:AAMP, ARF1, ATP5E, CLTC, GPS1, and PGK1. In another exemplaryembodiment, one or more of the following microRNAs are used asreferences by which the expression data of microRNAs are normalized:hsa-miR-106a; hsa-miR-146b-5p; hsa-miR-191; hsa-miR-19b; andhsa-miR-92a. The calibrated weighted average C_(T) or Cp measurementsfor each of the prognostic and predictive genes or microRNAs may benormalized relative to the mean of five or more reference genes ormicroRNAs.

Those skilled in the art will recognize that normalization may beachieved in numerous ways, and the techniques described above areintended only to be exemplary, not exhaustive.

Standardization of Expression Levels

The expression data used in the methods disclosed herein can bestandardized. Standardization refers to a process to effectively put allthe genes or microRNAs on a comparable scale. This is performed becausesome genes or microRNAs will exhibit more variation (a broader range ofexpression) than others. Standardization is performed by dividing eachexpression value by its standard deviation across all samples for thatgene or microRNA. Hazard ratios are then interpreted as the relativerisk of recurrence per 1 standard deviation increase in expression.

Kits of the Invention

The materials for use in the methods of the present invention are suitedfor preparation of kits produced in accordance with well-knownprocedures. The present disclosure thus provides kits comprising agents,which may include gene (or microRNA)-specific or gene (ormicroRNA)-selective probes and/or primers, for quantifying theexpression of the disclosed genes or microRNAs for predicting prognosticoutcome or response to treatment. Such kits may optionally containreagents for the extraction of RNA from tumor samples, in particularfixed paraffin-embedded tissue samples and/or reagents for RNAamplification. In addition, the kits may optionally comprise thereagent(s) with an identifying description or label or instructionsrelating to their use in the methods of the present invention. The kitsmay comprise containers (including microliter plates suitable for use inan automated implementation of the method), each with one or more of thevarious materials or reagents (typically in concentrated form) utilizedin the methods, including, for example, chromatographic columns,pre-fabricated microarrays, buffers, the appropriate nucleotidetriphosphates (e.g., dATP, dCTP, dGTP and dTTP; or rATP, rCTP, rGTP andUTP), reverse transcriptase, DNA polymerase, RNA polymerase, and one ormore probes and primers of the present invention (e.g., appropriatelength poly(T) or random primers linked to a promoter reactive with theRNA polymerase). Mathematical algorithms used to estimate or quantifyprognostic or predictive information are also properly potentialcomponents of kits.

Reports

The methods of this invention, when practiced for commercial diagnosticpurposes, generally produce a report or summary of information obtainedfrom the herein-described methods. For example, a report may includeinformation concerning expression levels of one or more genes and/ormicroRNAs, classification of the tumor or the patient's risk ofrecurrence, the patient's likely prognosis or risk classification,clinical and pathologic factors, and/or other information. The methodsand reports of this invention can further include storing the report ina database. The method can create a record in a database for the subjectand populate the record with data. The report may be a paper report, anauditory report, or an electronic record. The report may be displayedand/or stored on a computing device (e.g., handheld device, desktopcomputer, smart device, website, etc.). It is contemplated that thereport is provided to a physician and/or the patient. The receiving ofthe report can further include establishing a network connection to aserver computer that includes the data and report and requesting thedata and report from the server computer.

Computer Program

The values from the assays described above, such as expression data, canbe calculated and stored manually. Alternatively, the above-describedsteps can be completely or partially performed by a computer programproduct. The present invention thus provides a computer program productincluding a computer readable storage medium having a computer programstored on it. The program can, when read by a computer, execute relevantcalculations based on values obtained from analysis of one or morebiological sample from an individual (e.g., gene expression levels,normalization, standardization, thresholding, and conversion of valuesfrom assays to a score and/or text or graphical depiction of tumor stageand related information). The computer program product has storedtherein a computer program for performing the calculation.

The present disclosure provides systems for executing the programdescribed above, which system generally includes: a) a central computingenvironment; b) an input device, operatively connected to the computingenvironment, to receive patient data, wherein the patient data caninclude, for example, expression level or other value obtained from anassay using a biological sample from the patient, or microarray data, asdescribed in detail above; c) an output device, connected to thecomputing environment, to provide information to a user (e.g., medicalpersonnel); and d) an algorithm executed by the central computingenvironment (e.g., a processor), where the algorithm is executed basedon the data received by the input device, and wherein the algorithmcalculates an expression score, thresholding, or other functionsdescribed herein. The methods provided by the present invention may alsobe automated in whole or in part.

All aspects of the present invention may also be practiced such that alimited number of additional genes and/or microRNAs that areco-expressed or functionally related with the disclosed genes, forexample as evidenced by statistically meaningful Pearson and/or Spearmancorrelation coefficients, are included in a test in addition to and/orin place of disclosed genes.

Having described the invention, the same will be more readily understoodthrough reference to the following Examples, which are provided by wayof illustration, and are not intended to limit the invention in any way.

EXAMPLES Example 1: RNA Yield and Gene Expression Profiles in ProstateCancer Biopsy Cores

Clinical tools based on prostate needle core biopsies are needed toguide treatment planning at diagnosis for men with localized prostatecancer. Limiting tissue in needle core biopsy specimens posessignificant challenges to the development of molecular diagnostic tests.This study examined RNA extraction yields and gene expression profilesusing an RT-PCR assay to characterize RNA from manually micro-dissectedfixed paraffin embedded (FPE) prostate cancer needle biopsy cores. Italso investigated the association of RNA yields and gene expressionprofiles with Gleason score in these specimens.

Patients and Samples

This study determined the feasibility of gene expression profileanalysis in prostate cancer needle core biopsies by evaluating thequantity and quality of RNA extracted from fixed paraffin-embedded (FPE)prostate cancer needle core biopsy specimens. Forty-eight (48)formalin-fixed blocks from prostate needle core biopsy specimens wereused for this study. Classification of specimens was based oninterpretation of the Gleason score (2005 Int'l Society of UrologicalPathology Consensus Conference) and percentage tumor (<33%,33-66%, >66%) involvement as assessed by pathologists.

TABLE 1 Distribution of cases Gleason score ~<33% ~33-66% ~>66% CategoryTumor Tumor Tumor Low (≤6) 5 5 6 Intermediate (7) 5 5 6 High (8, 9, 10)5 5 6 Total 15 15 18

Assay Methods

Fourteen (14) serial 5 μm unstained sections from each FPE tissue blockwere included in the study. The first and last sections for each casewere H&E stained and histologically reviewed to confirm the presence oftumor and for tumor enrichment by manual micro-dissection.

RNA from enriched tumor samples was extracted using a manual RNAextraction process. RNA was quantitated using the RiboGreen® assay andtested for the presence of genomic DNA contamination. Samples withsufficient RNA yield and free of genomic DNA tested for gene expressionlevels of a 24-gene panel of reference and cancer-related genes usingquantitative RT-PCR. The expression was normalized to the average of 6reference genes (AAMP, ARF1, ATP5E, CLTC, EEF1A1, and GPX1).

Statistical Methods

Descriptive statistics and graphical displays were used to summarizestandard pathology metrics and gene expression, with stratification forGleason Score category and percentage tumor involvement category.Ordinal logistic regression was used to evaluate the relationshipbetween gene expression and Gleason Score category.

Results

The RNA yield per unit surface area ranged from 16 to 2406 ng/mm2.Higher RNA yield was observed in samples with higher percent tumorinvolvement (p=0.02) and higher Gleason score (p=0.01). RNA yield wassufficient (>200 ng) in 71% of cases to permit 96-well RT-PCR, with 87%of cases having >100 ng RNA yield. The study confirmed that geneexpression from prostate biopsies, as measured by qRT-PCR, wascomparable to FPET samples used in commercial molecular assays forbreast cancer. In addition, it was observed that greater biopsy RNAyields are found with higher Gleason score and higher percent tumorinvolvement. Nine genes were identified as significantly associated withGleason score (p<0.05) and there was a large dynamic range observed formany test genes.

Example 2: Gene Expression Analysis for Genes Associated with Prognosisin Prostate Cancer

Patients and Samples

Approximately 2600 patients with clinical stage T1/T2 prostate cancertreated with radical prostatectomy (RP) at the Cleveland Clinic between1987 and 2004 were identified. Patients were excluded from the studydesign if they received neo-adjuvant and/or adjuvant therapy, ifpre-surgical PSA levels were missing, or if no tumor block was availablefrom initial diagnosis. 127 patients with clinical recurrence and 374patients without clinical recurrence after radical prostatectomy wererandomly selected using a cohort sampling design. The specimens werestratified by T stage (T1, T2), year cohort (<1993, ≥1993), andprostatectomy Gleason score (low/intermediate, high). Of the 501 sampledpatients, 51 were excluded for insufficient tumor; 7 were excluded dueto clinical ineligibility; 2 were excluded due to poor quality of geneexpression data; and 10 were excluded because primary Gleason patternwas unavailable. Thus, this gene expression study included tissue anddata from 111 patients with clinical recurrence and 330 patients withoutclinical recurrence after radical prostatectomies performed between 1987and 2004 for treatment of early stage (T1, T2) prostate cancer.

Two fixed paraffin embedded (FPE) tissue specimens were obtained fromprostate tumor specimens in each patient. The sampling method (samplingmethod A or B) depended on whether the highest Gleason pattern is alsothe primary Gleason pattern. For each specimen selected, the invasivecancer cells were at least 5.0 mm in dimension, except in the instancesof pattern 5, where 2.2 mm was accepted. Specimens were spatiallydistinct where possible.

TABLE 2 Sampling Methods Sampling Method A Sampling Method B Forpatients whose prostatectomy primary For patients whose prostatectomyprimary Gleason pattern is also the highest Gleason Gleason pattern isnot the highest Gleason pattern pattern Specimen 1 (A1) = primaryGleason pattern Specimen 1 (B1) = highest Gleason pattern Select andmark largest focus (greatest cross- Select highest Gleason patterntissue from sectional area) of primary Gleason pattern spatiallydistinct area from specimen B2, if tissue. Invasive cancer area ≥5.0 mm.possible. Invasive cancer area at least 5.0 mm if selecting secondarypattern, at least 2.2 mm if selecting Gleason pattern 5. Specimen 2 (A2)= secondary Gleason pattern Specimen 2 (B2) = primary Gleason patternSelect and mark secondary Gleason pattern Select largest focus (greatestcross-sectional tissue from spatially distinct area from area) ofprimary Gleason pattern tissue. specimen A1. Invasive cancer area ≥5.0mm. Invasive cancer area ≥5.0 mm.

Histologically normal appearing tissue (NAT) adjacent to the tumorspecimen (also referred to in these Examples as “non-tumor tissue”) wasalso evaluated. Adjacent tissue was collected 3 mm from the tumor to 3mm from the edge of the FPET block. NAT was preferentially sampledadjacent to the primary Gleason pattern. In cases where there wasinsufficient NAT adjacent to the primary Gleason pattern, then NAT wassampled adjacent to the secondary or highest Gleason pattern (A2 or B 1)per the method set forth in Table 2. Six (6) 10 μm sections withbeginning H&E at 5 μm and ending unstained slide at 5 μm were preparedfrom each fixed paraffin-embedded tumor (FPET) block included in thestudy. All cases were histologically reviewed and manuallymicro-dissected to yield two enriched tumor samples and, where possible,one normal tissue sample adjacent to the tumor specimen.

Assay Method

In this study, RT-PCR analysis was used to determine RNA expressionlevels for 738 genes and chromosomal rearrangements (e.g., TMPRSS2-ERGfusion or other ETS family genes) in prostate cancer tissue andsurrounding NAT in patients with early-stage prostate cancer treatedwith radical prostatectomy.

The samples were quantified using the RiboGreen assay and a subsettested for presence of genomic DNA contamination. Samples were takeninto reverse transcription (RT) and quantitative polymerase chainreaction (qPCR). All analyses were conducted on reference-normalizedgene expression levels using the average of the of replicate wellcrossing point (CP) values for the 6 reference genes (AAMP, ARF1, ATP5E,CLTC, GPS1, PGK1).

Statistical Analysis and Results

Primary statistical analyses involved 111 patients with clinicalrecurrence and 330 patients without clinical recurrence after radicalprostatectomy for early-stage prostate cancer stratified by T-stage (T1,T2), year cohort (<1993, ≥1993), and prostatectomy Gleason score(low/intermediate, high). Gleason score categories are defined asfollows: low (Gleason score≤6), intermediate (Gleason score=7), and high(Gleason score≥8). A patient was included in a specified analysis if atleast one sample for that patient was evaluable. Unless otherwisestated, all hypothesis tests were reported using two-sided p-values. Themethod of Storey was applied to the resulting set of p-values to controlthe false discovery rate (FDR) at 20%. J. Storey, R. Tibshirani,Estimating the Positive False Discovery Rate Under Dependence, withApplications to DNA Microarrays, Dept. of Statistics, Stanford Univ.(2001).

Analysis of gene expression and recurrence-free interval was based onunivariate Cox Proportional Hazards (PH) models using maximum weightedpseudo-partial-likelihood estimators for each evaluable gene in the genelist (727 test genes and 5 reference genes). P-values were generatedusing Wald tests of the null hypothesis that the hazard ratio (HR) isone. Both unadjusted p-values and the q-value (smallest FDR at which thehypothesis test in question is rejected) were reported. Un-adjustedp-values<0.05 were considered statistically significant. Since two tumorspecimens were selected for each patient, this analysis was performedusing the 2 specimens from each patient as follows: (1) analysis usingthe primary Gleason pattern specimen from each patient (Specimens A1 andB2 as described in Table 2); (2) analysis using the highest Gleasonpattern specimen from each patient (Specimens A1 and B1 as described inTable 2).

Analysis of gene expression and Gleason pattern (3, 4, 5) was based onunivariate ordinal logistic regression models using weighted maximumlikelihood estimators for each gene in the gene list (727 test genes and5 reference genes). P-values were generated using a Wald test of thenull hypothesis that the odds ratio (OR) is one. Both unadjustedp-values and the q-value (smallest FDR at which the hypothesis test inquestion is rejected) were reported. Un-adjusted p-values<0.05 wereconsidered statistically significant. Since two tumor specimens wereselected for each patient, this analysis was performed using the 2specimens from each patient as follows: (1) analysis using the primaryGleason pattern specimen from each patient (Specimens A1 and B2 asdescribed in Table 2); (2) analysis using the highest Gleason patternspecimen from each patient (Specimens A1 and B1 as described in Table2).

It was determined whether there is a significant relationship betweencRFI and selected demographic, clinical, and pathology variables,including age, race, clinical tumor stage, pathologic tumor stage,location of selected tumor specimens within the prostate (peripheralversus transitional zone), PSA at the time of surgery, overall Gleasonscore from the radical prostatectomy, year of surgery, and specimenGleason pattern. Separately for each demographic or clinical variable,the relationship between the clinical covariate and cRFI was modeledusing univariate Cox PH regression using weighted pseudopartial-likelihood estimators and a p-value was generated using Wald'stest of the null hypothesis that the hazard ratio (HR) is one.Covariates with unadjusted p-values<0.2 may have been included in thecovariate-adjusted analyses.

It was determined whether there was a significant relationship betweeneach of the individual cancer-related genes and cRFI after controllingfor important demographic and clinical covariates. Separately for eachgene, the relationship between gene expression and cRFI was modeledusing multivariate Cox PH regression using weighted pseudopartial-likelihood estimators including important demographic andclinical variables as covariates. The independent contribution of geneexpression to the prediction of cRFI was tested by generating a p-valuefrom a Wald test using a model that included clinical covariates foreach nodule (specimens as defined in Table 2). Un-adjusted p-values<0.05were considered statistically significant.

Tables 3A and 3B provide genes significantly associated (p<0.05),positively or negatively, with Gleason pattern in the primary and/orhighest Gleason pattern. Increased expression of genes in Table 3A ispositively associated with higher Gleason score, while increasedexpression of genes in Table 3B are negatively associated with higherGleason score.

TABLE 3A Gene significantly (p < 0.05) associated with Gleason patternfor all specimens in the primary Gleason pattern or highest Gleasonpattern odds ratio (OR) >1.0 (Increased expression is positivelyassociated with higher Gleason Score) Official Primary Pattern HighestPattern Symbol OR p-value OR p-value ALCAM 1.73 <.001 1.36 0.009 ANLN1.35 0.027 APOC1 1.47 0.005 1.61 <.001 APOE 1.87 <.001 2.15 <.001 ASAP21.53 0.005 ASPN 2.62 <.001 2.13 <.001 ATP5E 1.35 0.035 AURKA 1.44 0.010AURKB 1.59 <.001 1.56 <.001 BAX 1.43 0.006 BGN 2.58 <.001 2.82 <.001BIRC5 1.45 0.003 1.79 <.001 BMP6 2.37 <.001 1.68 <.001 BMPR1B 1.58 0.002BRCA2 1.45 0.013 BUB1 1.73 <.001 1.57 <.001 CACNA1D 1.31 0.045 1.310.033 CADPS 1.30 0.023 CCNB1 1.43 0.023 CCNE2 1.52 0.003 1.32 0.035CD276 2.20 <.001 1.83 <.001 CD68 1.36 0.022 CDC20 1.69 <.001 1.95 <.001CDC6 1.38 0.024 1.46 <.001 CDH11 1.30 0.029 CDKN2B 1.55 0.001 1.33 0.023CDKN2C 1.62 <.001 1.52 <.001 CDKN3 1.39 0.010 1.50 0.002 CENPF 1.96<.001 1.71 <.001 CHRAC1 1.34 0.022 CLDN3 1.37 0.029 COL1A1 2.23 <.0012.22 <.001 COL1A2 1.42 0.005 COL3A1 1.90 <.001 2.13 <.001 COL8A1 1.88<.001 2.35 <.001 CRISP3 1.33 0.040 1.26 0.050 CTHRC1 2.01 <.001 1.61<.001 CTNND2 1.48 0.007 1.37 0.011 DAPK1 1.44 0.014 DIAPH1 1.34 0.0321.79 <.001 DIO2 1.56 0.001 DLL4 1.38 0.026 1.53 <.001 ECE1 1.54 0.0121.40 0.012 ENY2 1.35 0.046 1.35 0.012 EZH2 1.39 0.040 F2R 2.37 <.0012.60 <.001 FAM49B 1.57 0.002 1.33 0.025 FAP 2.36 <.001 1.89 <.001 FCGR3A2.10 <.001 1.83 <.001 GNPTAB 1.78 <.001 1.54 <.001 GSK3B 1.39 0.018 HRAS1.62 0.003 HSD17B4 2.91 <.001 1.57 <.001 HSPA8 1.48 0.012 1.34 0.023IFI30 1.64 <.001 1.45 0.013 IGFBP3 1.29 0.037 IL11 1.52 0.001 1.31 0.036INHBA 2.55 <.001 2.30 <.001 ITGA4 1.35 0.028 JAG1 1.68 <.001 1.40 0.005KCNN2 1.50 0.004 KCTD12 1.38 0.012 KHDRBS3 1.85 <.001 1.72 <.001 KIF4A1.50 0.010 1.50 <.001 KLK14 1.49 0.001 1.35 <.001 KPNA2 1.68 0.004 1.650.001 KRT2 1.33 0.022 KRT75 1.27 0.028 LAMC1 1.44 0.029 LAPTM5 1.360.025 1.31 0.042 LTBP2 1.42 0.023 1.66 <.001 MANF 1.34 0.019 MAOA 1.550.003 1.50 <.001 MAP3K5 1.55 0.006 1.44 0.001 MDK 1.47 0.013 1.29 0.041MDM2 1.31 0.026 MELK 1.64 <.001 1.64 <.001 MMP11 2.33 <.001 1.66 <.001MYBL2 1.41 0.007 1.54 <.001 MYO6 1.32 0.017 NETO2 1.36 0.018 NOX4 1.84<.001 1.73 <.001 NPM1 1.68 0.001 NRIP3 1.36 0.009 NRP1 1.80 0.001 1.360.019 OSM 1.33 0.046 PATE1 1.38 0.032 PECAM1 1.38 0.021 1.31 0.035 PGD1.56 0.010 PLK1 1.51 0.004 1.49 0.002 PLOD2 1.29 0.027 POSTN 1.70 0.0471.55 0.006 PPP3CA 1.38 0.037 1.37 0.006 PTK6 1.45 0.007 1.53 <.001 PTTG11.51 <.001 RAB31 1.31 0.030 RAD21 2.05 <.001 1.38 0.020 RAD51 1.46 0.0021.26 0.035 RAF1 1.46 0.017 RALBP1 1.37 0.043 RHOC 1.33 0.021 ROBO2 1.520.003 1.41 0.006 RRM2 1.77 <.001 1.50 <.001 SAT1 1.67 0.002 1.61 <.001SDC1 1.66 0.001 1.46 0.014 SEC14L1 1.53 0.003 1.62 <.001 SESN3 1.76<.001 1.45 <.001 SFRP4 2.69 <.001 2.03 <.001 SHMT2 1.69 0.007 1.45 0.003SKIL 1.46 0.005 SOX4 1.42 0.016 1.27 0.031 SPARC 1.40 0.024 1.55 <.001SPINK1 1.29 0.002 SPP1 1.51 0.002 1.80 <.001 TFDP1 1.48 0.014 THBS2 1.87<.001 1.65 <.001 THY1 1.58 0.003 1.64 <.001 TK1 1.79 <.001 1.42 0.001TOP2A 2.30 <.001 2.01 <.001 TPD52 1.95 <.001 1.30 0.037 TPX2 2.12 <.0011.86 <.001 TYMP 1.36 0.020 TYMS 1.39 0.012 1.31 0.036 UBE2C 1.66 <.0011.65 <.001 UBE2T 1.59 <.001 1.33 0.017 UGDH 1.28 0.049 UGT2B15 1.460.001 1.25 0.045 UHRF1 1.95 <.001 1.62 <.001 VDR 1.43 0.010 1.39 0.018WNT5A 1.54 0.001 1.44 0.013

TABLE 3B Gene significantly (p < 0.05) associated with Gleason patternfor all specimens in the primary Gleason pattern or highest Gleasonpattern odds ratio (OR) <1.0 (Increased expression is negativelyassociated with higher Gleason score) Official Primary Pattern HighestPattern Symbol OR p-value OR p-value ABCA5 0.78 0.041 ABCG2 0.65 0.0010.72 0.012 ACOX2 0.44 <.001 0.53 <.001 ADH5 0.45 <.001 0.42 <.001 AFAP10.79 0.038 AIG1 0.77 0.024 AKAP1 0.63 0.002 AKR1C1 0.66 0.003 0.63 <.001AKT3 0.68 0.006 0.77 0.010 ALDH1A2 0.28 <.001 0.33 <.001 ALKBH3 0.770.040 0.77 0.029 AMPD3 0.67 0.007 ANPEP 0.68 0.008 0.59 <.001 ANXA2 0.720.018 APC 0.69 0.002 AXIN2 0.46 <.001 0.54 <.001 AZGP1 0.52 <.001 0.53<.001 BIK 0.69 0.006 0.73 0.003 BIN1 0.43 <.001 0.61 <.001 BTG3 0.790.030 BTRC 0.48 <.001 0.62 <.001 C7 0.37 <.001 0.55 <.001 CADM1 0.56<.001 0.69 0.001 CAV1 0.58 0.002 0.70 0.009 CAV2 0.65 0.029 CCNH 0.670.006 0.77 0.048 CD164 0.59 0.003 0.57 <.001 CDC25B 0.77 0.035 CDH1 0.66<.001 CDK2 0.71 0.003 CDKN1C 0.58 <.001 0.57 <.001 CDS2 0.69 0.002 CHN10.66 0.002 COL6A1 0.44 <.001 0.66 <.001 COL6A3 0.66 0.006 CSRP1 0.420.006 CTGF 0.74 0.043 CTNNA1 0.70 <.001 0.83 0.018 CTNNB1 0.70 0.019CTNND1 0.75 0.028 CUL1 0.74 0.011 CXCL12 0.54 <.001 0.74 0.006 CYP3A50.52 <.001 0.66 0.003 CYR61 0.64 0.004 0.68 0.005 DDR2 0.57 0.002 0.730.004 DES 0.34 <.001 0.58 <.001 DLGAP1 0.54 <.001 0.62 <.001 DNM3 0.670.004 DPP4 0.41 <.001 0.53 <.001 DPT 0.28 <.001 0.48 <.001 DUSP1 0.59<.001 0.63 <.001 EDNRA 0.64 0.004 0.74 0.008 EGF 0.71 0.012 EGR1 0.59<.001 0.67 0.009 EGR3 0.72 0.026 0.71 0.025 EIF5 0.76 0.025 ELK4 0.580.001 0.70 0.008 ENPP2 0.66 0.002 0.70 0.005 EPHA3 0.65 0.006 EPHB2 0.60<.001 0.78 0.023 EPHB4 0.75 0.046 0.73 0.006 ERBB3 0.76 0.040 0.75 0.013ERBB4 0.74 0.023 ERCC1 0.63 <.001 0.77 0.016 FAAH 0.67 0.003 0.71 0.010FAM107A 0.35 <.001 0.59 <.001 FAM13C 0.37 <.001 0.48 <.001 FAS 0.730.019 0.72 0.008 FGF10 0.53 <.001 0.58 <.001 FGF7 0.52 <.001 0.59 <.001FGFR2 0.60 <.001 0.59 <.001 FKBP5 0.70 0.039 0.68 0.003 FLNA 0.39 <.0010.56 <.001 FLNC 0.33 <.001 0.52 <.001 FOS 0.58 <.001 0.66 0.005 FOXO10.57 <.001 0.67 <.001 FOXQ1 0.74 0.023 GADD45B 0.62 0.002 0.71 0.010 GHR0.62 0.002 0.72 0.009 GNRH1 0.74 0.049 0.75 0.026 GPM6B 0.48 <.001 0.68<.001 GPS1 0.68 0.003 GSN 0.46 <.001 0.77 0.027 GSTM1 0.44 <.001 0.62<.001 GSTM2 0.29 <.001 0.49 <.001 HGD 0.77 0.020 HIRIP3 0.75 0.034 HK10.48 <.001 0.66 0.001 HLF 0.42 <.001 0.55 <.001 HNF1B 0.67 0.006 0.740.010 HPS1 0.66 0.001 0.65 <.001 HSP90AB1 0.75 0.042 HSPA5 0.70 0.011HSPB2 0.52 <.001 0.70 0.004 IGF1 0.35 <.001 0.59 <.001 IGF2 0.48 <.0010.70 0.005 IGFBP2 0.61 <.001 0.77 0.044 IGFBP5 0.63 <.001 IGFBP6 0.45<.001 0.64 <.001 IL6ST 0.55 0.004 0.63 <.001 ILK 0.40 <.001 0.57 <.001ING5 0.56 <.001 0.78 0.033 ITGA1 0.56 0.004 0.61 <.001 ITGA3 0.78 0.035ITGA5 0.71 0.019 0.75 0.017 ITGA7 0.37 <.001 0.52 <.001 ITGB3 0.63 0.0030.70 0.005 ITPR1 0.46 <.001 0.64 <.001 ITPR3 0.70 0.013 ITSN1 0.62 0.001JUN 0.48 <.001 0.60 <.001 JUNB 0.72 0.025 KIT 0.51 <.001 0.68 0.007 KLC10.58 <.001 KLK1 0.69 0.028 0.66 0.003 KLK2 0.60 <.001 KLK3 0.63 <.0010.69 0.012 KRT15 0.56 <.001 0.60 <.001 KRT18 0.74 0.034 KRT5 0.64 <.0010.62 <.001 LAMA4 0.47 <.001 0.73 0.010 LAMB3 0.73 0.018 0.69 0.003LGALS3 0.59 0.003 0.54 <.001 LIG3 0.75 0.044 MAP3K7 0.66 0.003 0.790.031 MCM3 0.73 0.013 0.80 0.034 MGMT 0.61 0.001 0.71 0.007 MGST1 0.750.017 MLXIP 0.70 0.013 MMP2 0.57 <.001 0.72 0.010 MMP7 0.69 0.009 MPPED20.70 0.009 0.59 <.001 MSH6 0.78 0.046 MTA1 0.69 0.007 MTSS1 0.55 <.0010.54 <.001 MYBPC1 0.45 <.001 0.45 <.001 NCAM1 0.51 <.001 0.65 <.001NCAPD3 0.42 <.001 0.53 <.001 NCOR2 0.68 0.002 NDUFS5 0.66 0.001 0.700.013 NEXN 0.48 <.001 0.62 <.001 NFAT5 0.55 <.001 0.67 0.001 NFKBIA 0.790.048 NRG1 0.58 0.001 0.62 0.001 OLFML3 0.42 <.001 0.58 <.001 OMD 0.670.004 0.71 0.004 OR51E2 0.65 <.001 0.76 0.007 PAGE4 0.27 <.001 0.46<.001 PCA3 0.68 0.004 PCDHGB7 0.70 0.025 0.65 <.001 PGF 0.62 0.001 PGR0.63 0.028 PHTF2 0.69 0.033 PLP2 0.54 <.001 0.71 0.003 PPAP2B 0.41 <.0010.54 <.001 PPP1R12A 0.48 <.001 0.60 <.001 PRIMA1 0.62 0.003 0.65 <.001PRKAR1B 0.70 0.009 PRKAR2B 0.79 0.038 PRKCA 0.37 <.001 0.55 <.001 PRKCB0.47 <.001 0.56 <.001 PTCH1 0.70 0.021 PTEN 0.66 0.010 0.64 <.001 PTGER30.76 0.015 PTGS2 0.70 0.013 0.68 0.005 PTH1R 0.48 <.001 PTK2B 0.67 0.0140.69 0.002 PYCARD 0.72 0.023 RAB27A 0.76 0.017 RAGE 0.77 0.040 0.57<.001 RARB 0.66 0.002 0.69 0.002 RECK 0.65 <.001 RHOA 0.73 0.043 RHOB0.61 0.005 0.62 <.001 RND3 0.63 0.006 0.66 <.001 SDHC 0.69 0.002 SEC23A0.61 <.001 0.74 0.010 SEMA3A 0.49 <.001 0.55 <.001 SERPINA3 0.70 0.0340.75 0.020 SH3RF2 0.33 <.001 0.42 <.001 SLC22A3 0.23 <.001 0.37 <.001SMAD4 0.33 <.001 0.39 <.001 SMARCC2 0.62 0.003 0.74 0.008 SMO 0.53 <.0010.73 0.009 SORBS1 0.40 <.001 0.55 <.001 SPARCL1 0.42 <.001 0.63 <.001SRD5A2 0.28 <.001 0.37 <.001 ST5 0.52 <.001 0.63 <.001 STAT5A 0.60 <.0010.75 0.020 STAT5B 0.54 <.001 0.65 <.001 STS 0.78 0.035 SUMO1 0.75 0.0170.71 0.002 SVIL 0.45 <.001 0.62 <.001 TARP 0.72 0.017 TGFB1I1 0.37 <.0010.53 <.001 TGFB2 0.61 0.025 0.59 <.001 TGFB3 0.46 <.001 0.60 <.001 TIMP20.62 0.001 TIMP3 0.55 <.001 0.76 0.019 TMPRSS2 0.71 0.014 TNF 0.65 0.010TNFRSF10A 0.71 0.014 0.74 0.010 TNFRSF10B 0.74 0.030 0.73 0.016 TNFSF100.69 0.004 TP53 0.73 0.011 TP63 0.62 <.001 0.68 0.003 TPM1 0.43 <.0010.47 <.001 TPM2 0.30 <.001 0.47 <.001 TPP2 0.58 <.001 0.69 0.001 TRA2A0.71 0.006 TRAF3IP2 0.50 <.001 0.63 <.001 TRO 0.40 <.001 0.59 <.001TRPC6 0.73 0.030 TRPV6 0.80 0.047 VCL 0.44 <.001 0.55 <.001 VEGFB 0.730.029 VIM 0.72 0.013 VTI1B 0.78 0.046 WDR19 0.65 <.001 WFDC1 0.50 <.0010.72 0.010 YY1 0.75 0.045 ZFHX3 0.52 <.001 0.54 <.001 ZFP36 0.65 0.0040.69 0.012 ZNF827 0.59 <.001 0.69 0.004

To identify genes associated with recurrence (cRFI, bRFI) in the primaryand the highest Gleason pattern, each of 727 genes were analyzed inunivariate models using specimens A1 and B2 (see Table 2, above). Tables4A and 4B provide genes that were associated, positively or negatively,with cRFI and/or bRFI in the primary and/or highest Gleason pattern.Increased expression of genes in Table 4A is negatively associated withgood prognosis, while increased expression of genes in Table 4B ispositively associated with good prognosis.

TABLE 4A Genes significantly (p < 0.05) associated with cRFI or bRFI inthe primary Gleason pattern or highest Gleason pattern with hazard ratio(HR) >1.0 (increased expression is negatively associated with goodprognosis) cRFI cRFI bRFI bRFI Primary Highest Primary Highest PatternPattern Pattern Pattern Official p- p- p- p- Symbol HR value HR value HRvalue HR value AKR1C3 1.304 0.022 1.312 0.013 ANLN 1.379 0.002 1.579<.001 1.465 <.001 1.623 <.001 AQP2 1.184 0.027 1.276 <.001 ASAP2 1.4420.006 ASPN 2.272 <.001 2.106 <.001 1.861 <.001 1.895 <.001 ATP5E 1.4140.013 1.538 <.001 BAG5 1.263 0.044 BAX 1.332 0.026 1.327 0.012 1.4380.002 BGN 1.947 <.001 2.061 <.001 1.339 0.017 BIRC5 1.497 <.001 1.567<.001 1.478 <.001 1.575 <.001 BMP6 1.705 <.001 2.016 <.001 1.418 0.0041.541 <.001 BMPR1B 1.401 0.013 1.325 0.016 BRCA2 1.259 0.007 BUB1 1.411<.001 1.435 <.001 1.352 <.001 1.242 0.002 CADPS 1.387 0.009 1.294 0.027CCNB1 1.296 0.016 1.376 0.002 CCNE2 1.468 <.001 1.649 <.001 1.729 <.0011.563 <.001 CD276 1.678 <.001 1.832 <.001 1.581 <.001 1.385 0.002 CDC201.547 <.001 1.671 <.001 1.446 <.001 1.540 <.001 CDC6 1.400 0.003 1.2900.030 1.403 0.002 1.276 0.019 CDH7 1.403 0.003 1.413 0.002 CDKN2B 1.569<.001 1.752 <.001 1.333 0.017 1.347 0.006 CDKN2C 1.612 <.001 1.780 <.0011.323 0.005 1.335 0.004 CDKN3 1.384 <.001 1.255 0.024 1.285 0.003 1.2160.028 CENPF 1.578 <.001 1.692 <.001 1.740 <.001 1.705 <.001 CKS2 1.3900.007 1.418 0.005 1.291 0.018 CLTC 1.368 0.045 COL1A1 1.873 <.001 2.103<.001 1.491 <.001 1.472 <.001 COL1A2 1.462 0.001 COL3A1 1.827 <.0012.005 <.001 1.302 0.012 1.298 0.018 COL4A1 1.490 0.002 1.613 <.001COL8A1 1.692 <.001 1.926 <.001 1.307 0.013 1.317 0.010 CRISP3 1.4250.001 1.467 <.001 1.242 0.045 CTHRC1 1.505 0.002 2.025 <.001 1.425 0.0031.369 0.005 CTNND2 1.412 0.003 CXCR4 1.312 0.023 1.355 0.008 DDIT4 1.543<.001 1.763 <.001 DYNLL1 1.290 0.039 1.201 0.004 EIF3H 1.428 0.012 ENY21.361 0.014 1.392 0.008 1.371 0.001 EZH2 1.311 0.010 F2R 1.773 <.0011.695 <.001 1.495 <.001 1.277 0.018 FADD 1.292 0.018 FAM171B 1.285 0.036FAP 1.455 0.004 1.560 0.001 1.298 0.022 1.274 0.038 FASN 1.263 0.035FCGR3A 1.654 <.001 1.253 0.033 1.350 0.007 FGF5 1.219 0.030 GNPTAB 1.3880.007 1.503 0.003 1.355 0.005 1.434 0.002 GPR68 1.361 0.008 GREM1 1.4700.003 1.716 <.001 1.421 0.003 1.316 0.017 HDAC1 1.290 0.025 HDAC9 1.3950.012 HRAS 1.424 0.006 1.447 0.020 HSD17B4 1.342 0.019 1.282 0.026 1.569<.001 1.390 0.002 HSPA8 1.290 0.034 IGFBP3 1.333 0.022 1.442 0.003 1.2530.040 1.323 0.005 INHBA 2.368 <.001 2.765 <.001 1.466 0.002 1.671 <.001JAG1 1.359 0.006 1.367 0.005 1.259 0.024 KCNN2 1.361 0.011 1.413 0.0051.312 0.017 1.281 0.030 KHDRBS3 1.387 0.006 1.601 <.001 1.573 <.0011.353 0.006 KIAA0196 1.249 0.037 KIF4A 1.212 0.016 1.149 0.040 1.2780.003 KLK14 1.167 0.023 1.180 0.007 KPNA2 1.425 0.009 1.353 0.005 1.3050.019 KRT75 1.164 0.028 LAMA3 1.327 0.011 LAMB1 1.347 0.019 LAMC1 1.5550.001 1.310 0.030 1.349 0.014 LIMS1 1.275 0.022 LOX 1.358 0.003 1.410<.001 LTBP2 1.396 0.009 1.656 <.001 1.278 0.022 LUM 1.315 0.021 MANF1.660 <.001 1.323 0.011 MCM2 1.345 0.011 1.387 0.014 MCM6 1.307 0.0231.352 0.008 1.244 0.039 MELK 1.293 0.014 1.401 <.001 1.501 <.001 1.2560.012 MMP11 1.680 <.001 1.474 <.001 1.489 <.001 1.257 0.030 MRPL13 1.2600.025 MSH2 1.295 0.027 MYBL2 1.664 <.001 1.670 <.001 1.399 <.001 1.431<.001 MYO6 1.301 0.033 NETO2 1.412 0.004 1.302 0.027 1.298 0.009 NFKB11.236 0.050 NOX4 1.492 <.001 1.507 0.001 1.555 <.001 1.262 0.019 NPM11.287 0.036 NRIP3 1.219 0.031 1.218 0.018 NRP1 1.482 0.002 1.245 0.041OLFML2B 1.362 0.015 OR51E1 1.531 <.001 1.488 0.003 PAK6 1.269 0.033PATE1 1.308 <.001 1.332 <.001 1.164 0.044 PCNA 1.278 0.020 PEX10 1.4360.005 1.393 0.009 PGD 1.298 0.048 1.579 <.001 PGK1 1.274 0.023 1.2620.009 PLA2G7 1.315 0.011 1.346 0.005 PLAU 1.319 0.010 PLK1 1.309 0.0211.563 <.001 1.410 0.002 1.372 0.003 PLOD2 1.284 0.019 1.272 0.014 1.3320.005 POSTN 1.599 <.001 1.514 0.002 1.391 0.005 PPP3CA 1.402 0.007 1.3160.018 PSMD13 1.278 0.040 1.297 0.033 1.279 0.017 1.373 0.004 PTK6 1.640<.001 1.932 <.001 1.369 0.001 1.406 <.001 PTTG1 1.409 <.001 1.510 <.0011.347 0.001 1.558 <.001 RAD21 1.315 0.035 1.402 0.004 1.589 <.001 1.439<.001 RAF1 1.503 0.002 RALA 1.521 0.004 1.403 0.007 1.563 <.001 1.2290.040 RALBP1 1.277 0.033 RGS7 1.154 0.015 1.266 0.010 RRM1 1.570 0.0011.602 <.001 RRM2 1.368 <.001 1.289 0.004 1.396 <.001 1.230 0.015 SAT11.482 0.016 1.403 0.030 SDC1 1.340 0.018 1.396 0.018 SEC14L1 1.260 0.0481.360 0.002 SESN3 1.485 <.001 1.631 <.001 1.232 0.047 1.292 0.014 SFRP41.800 <.001 1.814 <.001 1.496 <.001 1.289 0.027 SHMT2 1.807 <.001 1.658<.001 1.673 <.001 1.548 <.001 SKIL 1.327 0.008 SLC25A21 1.398 0.0011.285 0.018 SOX4 1.286 0.020 1.280 0.030 SPARC 1.539 <.001 1.842 <.0011.269 0.026 SPP1 1.322 0.022 SQLE 1.359 0.020 1.270 0.036 STMN1 1.4020.007 1.446 0.005 1.279 0.031 SULF1 1.587 <.001 TAF2 1.273 0.027 TFDP11.328 0.021 1.400 0.005 1.416 0.001 THBS2 1.812 <.001 1.960 <.001 1.3200.012 1.256 0.038 THY1 1.362 0.020 1.662 <.001 TK1 1.251 0.011 1.377<.001 1.401 <.001 TOP2A 1.670 <.001 1.920 <.001 1.869 <.001 1.927 <.001TPD52 1.324 0.011 1.366 0.002 1.351 0.005 TPX2 1.884 <.001 2.154 <.0011.874 <.001 1.794 <.001 UAP1 1.244 0.044 UBE2C 1.403 <.001 1.541 <.0011.306 0.002 1.323 <.001 UBE2T 1.667 <.001 1.282 0.023 1.502 <.001 1.2980.005 UGT2B15 1.295 0.001 1.275 0.002 UGT2B17 1.294 0.025 UHRF1 1.454<.001 1.531 <.001 1.257 0.029 VCPIP1 1.390 0.009 1.414 0.004 1.294 0.0211.283 0.021 WNT5A 1.274 0.038 1.298 0.020 XIAP 1.464 0.006 ZMYND8 1.2770.048 ZWINT 1.259 0.047

TABLE 4B Genes significantly (p < 0.05) associated with cRFI or bRFI inthe primary Gleason pattern or highest Gleason pattern with hazard ratio(HR) <1.0 (increased expression is positively associated with goodprognosis) cRFI cRFI bRFI bRFI Primary Highest Primary Highest PatternPattern Pattern Pattern Official p- p- p- p- Symbol HR value HR value HRvalue HR value AAMP 0.564 <.001 0.571 <.001 0.764 0.037 0.786 0.034ABCA5 0.755 <.001 0.695 <.001 0.800 0.006 ABCB1 0.777 0.026 ABCG2 0.7880.033 0.784 0.040 0.803 0.018 0.750 0.004 ABHD2 0.734 0.011 ACE 0.7820.048 ACOX2 0.639 <.001 0.631 <.001 0.713 <.001 0.716 0.002 ADH5 0.625<.001 0.637 <.001 0.753 0.026 AKAP1 0.764 0.006 0.800 0.005 0.837 0.046AKR1C1 0.773 0.033 0.802 0.032 AKT1 0.714 0.005 AKT3 0.811 0.015 0.8090.021 ALDH1A2 0.606 <.001 0.498 <.001 0.613 <.001 0.624 <.001 AMPD30.793 0.024 ANPEP 0.584 <.001 0.493 <.001 ANXA2 0.753 0.013 0.781 0.0360.762 0.008 0.795 0.032 APRT 0.758 0.026 0.780 0.044 0.746 0.008 ATXN10.673 0.001 0.776 0.029 0.809 0.031 0.812 0.043 AXIN2 0.674 <.001 0.571<.001 0.776 0.005 0.757 0.005 AZGP1 0.585 <.001 0.652 <.001 0.664 <.0010.746 <.001 BAD 0.765 0.023 BCL2 0.788 0.033 0.778 0.036 BDKRB1 0.7280.039 BIK 0.712 0.005 BIN1 0.607 <.001 0.724 0.002 0.726 <.001 0.8340.034 BTG3 0.847 0.034 BTRC 0.688 0.001 0.713 0.003 C7 0.589 <.001 0.639<.001 0.629 <.001 0.691 <.001 CADM1 0.546 <.001 0.529 <.001 0.743 0.0080.769 0.015 CASP1 0.769 0.014 0.799 0.028 0.799 0.010 0.815 0.018 CAV10.736 0.011 0.711 0.005 0.675 <.001 0.743 0.006 CAV2 0.636 0.010 0.6480.012 0.685 0.012 CCL2 0.759 0.029 0.764 0.024 CCNH 0.689 <.001 0.700<.001 CD164 0.664 <.001 0.651 <.001 CD1A 0.687 0.004 CD44 0.545 <.0010.600 <.001 0.788 0.018 0.799 0.023 CD82 0.771 0.009 0.748 0.004 CDC25B0.755 0.006 0.817 0.025 CDK14 0.845 0.043 CDK2 0.819 0.032 CDK3 0.7330.005 0.772 0.006 0.838 0.017 CDKN1A 0.766 0.041 CDKN1C 0.662 <.0010.712 0.002 0.693 <.001 0.761 0.009 CHN1 0.788 0.036 COL6A1 0.608 <.0010.767 0.013 0.706 <.001 0.775 0.007 CSF1 0.626 <.001 0.709 0.003 CSK0.837 0.029 CSRP1 0.793 0.024 0.782 0.019 CTNNB1 0.898 0.042 0.885 <.001CTSB 0.701 0.004 0.713 0.007 0.715 0.002 0.803 0.038 CTSK 0.815 0.042CXCL12 0.652 <.001 0.802 0.044 0.711 0.001 CYP3A5 0.463 <.001 0.436<.001 0.727 0.003 CYR61 0.652 0.002 0.676 0.002 DAP 0.761 0.026 0.7750.025 0.802 0.048 DARC 0.725 0.005 0.792 0.032 DDR2 0.719 0.001 0.7630.008 DES 0.619 <.001 0.737 0.005 0.638 <.001 0.793 0.017 DHRS9 0.6420.003 DHX9 0.888 <.001 DLC1 0.710 0.007 0.715 0.009 DLGAP1 0.613 <.0010.551 <.001 0.779 0.049 DNM3 0.679 <.001 0.812 0.037 DPP4 0.591 <.0010.613 <.001 0.761 0.003 DPT 0.613 <.001 0.576 <.001 0.647 <.001 0.677<.001 DUSP1 0.662 0.001 0.665 0.001 0.785 0.024 DUSP6 0.713 0.005 0.6680.002 EDNRA 0.702 0.002 0.779 0.036 EGF 0.738 0.028 EGR1 0.569 <.0010.577 <.001 0.782 0.022 EGR3 0.601 <.001 0.619 <.001 0.800 0.038 EIF2S30.756 0.015 EIF5 0.776 0.023 0.787 0.028 ELK4 0.628 <.001 0.658 <.001EPHA2 0.720 0.011 0.663 0.004 EPHA3 0.727 0.003 0.772 0.005 ERBB2 0.7860.019 0.738 0.003 0.815 0.041 ERBB3 0.728 0.002 0.711 0.002 0.828 0.0430.813 0.023 ERCC1 0.771 0.023 0.725 0.007 0.806 0.049 0.704 0.002 EREG0.754 0.016 0.777 0.034 ESR2 0.731 0.026 FAAH 0.708 0.004 0.758 0.0120.784 0.031 0.774 0.007 FAM107A 0.517 <.001 0.576 <.001 0.642 <.0010.656 <.001 FAM13C 0.568 <.001 0.526 <.001 0.739 0.002 0.639 <.001 FAS0.755 0.014 FASLG 0.706 0.021 FGF10 0.653 <.001 0.685 <.001 0.766 0.022FGF17 0.746 0.023 0.781 0.015 0.805 0.028 FGF7 0.794 0.030 0.820 0.0370.811 0.040 FGFR2 0.683 <.001 0.686 <.001 0.674 <.001 0.703 <.001 FKBP50.676 0.001 FLNA 0.653 <.001 0.741 0.010 0.682 <.001 0.771 0.016 FLNC0.751 0.029 0.779 0.047 0.663 <.001 0.725 <.001 FLT1 0.799 0.044 FOS0.566 <.001 0.543 <.001 0.757 0.006 FOXO1 0.816 0.039 0.798 0.023 FOXQ10.753 0.017 0.757 0.024 0.804 0.018 FYN 0.779 0.031 GADD45B 0.590 <.0010.619 <.001 GDF15 0.759 0.019 0.794 0.048 GHR 0.702 0.005 0.630 <.0010.673 <.001 0.590 <.001 GNRH1 0.742 0.014 GPM6B 0.653 <.001 0.633 <.0010.696 <.001 0.768 0.007 GSN 0.570 <.001 0.697 0.001 0.697 <.001 0.7580.005 GSTM1 0.612 <.001 0.588 <.001 0.718 <.001 0.801 0.020 GSTM2 0.540<.001 0.630 <.001 0.602 <.001 0.706 <.001 HGD 0.796 0.020 0.736 0.002HIRIP3 0.753 0.011 0.824 0.050 HK1 0.684 <.001 0.683 <.001 0.799 0.0110.804 0.014 HLA-G 0.726 0.022 HLF 0.555 <.001 0.582 <.001 0.703 <.0010.702 <.001 HNF1B 0.690 <.001 0.585 <.001 HPS1 0.744 0.003 0.784 0.0200.836 0.047 HSD3B2 0.733 0.016 HSP90AB1 0.801 0.036 HSPA5 0.776 0.034HSPB1 0.813 0.020 HSPB2 0.762 0.037 0.699 0.002 0.783 0.034 HSPG2 0.7940.044 ICAM1 0.743 0.024 0.768 0.040 IER3 0.686 0.002 0.663 <.001 IFIT10.649 <.001 0.761 0.026 IGF1 0.634 <.001 0.537 <.001 0.696 <.001 0.688<.001 IGF2 0.732 0.004 IGFBP2 0.548 <.001 0.620 <.001 IGFBP5 0.681 <.001IGFBP6 0.577 <.001 0.675 <.001 IL1B 0.712 0.005 0.742 0.009 IL6 0.7630.028 IL6R 0.791 0.039 IL6ST 0.585 <.001 0.639 <.001 0.730 0.002 0.7680.006 IL8 0.624 <.001 0.662 0.001 ILK 0.712 0.009 0.728 0.012 0.7900.047 0.790 0.042 ING5 0.625 <.001 0.658 <.001 0.728 0.002 ITGA5 0.7280.006 0.803 0.039 ITGA6 0.779 0.007 0.775 0.006 ITGA7 0.584 <.001 0.7000.001 0.656 <.001 0.786 0.014 ITGAD 0.657 0.020 ITGB4 0.718 0.007 0.689<.001 0.818 0.041 ITGB5 0.801 0.050 ITPR1 0.707 0.001 JUN 0.556 <.0010.574 <.001 0.754 0.008 JUNB 0.730 0.017 0.715 0.010 KIT 0.644 0.0040.705 0.019 0.605 <.001 0.659 0.001 KLC1 0.692 0.003 0.774 0.024 0.7470.008 KLF6 0.770 0.032 0.776 0.039 KLK1 0.646 <.001 0.652 0.001 0.7840.037 KLK10 0.716 0.006 KLK2 0.647 <.001 0.628 <.001 0.786 0.009 KLK30.706 <.001 0.748 <.001 0.845 0.018 KRT1 0.734 0.024 KRT15 0.627 <.0010.526 <.001 0.704 <.001 0.782 0.029 KRT18 0.624 <.001 0.617 <.001 0.7380.005 0.760 0.005 KRT5 0.640 <.001 0.550 <.001 0.740 <.001 0.798 0.023KRT8 0.716 0.006 0.744 0.008 L1CAM 0.738 0.021 0.692 0.009 0.761 0.036LAG3 0.741 0.013 0.729 0.011 LAMA4 0.686 0.011 0.592 0.003 LAMA5 0.7860.025 LAMB3 0.661 <.001 0.617 <.001 0.734 <.001 LGALS3 0.618 <.001 0.7020.001 0.734 0.001 0.793 0.012 LIG3 0.705 0.008 0.615 <.001 LRP1 0.7860.050 0.795 0.023 0.770 0.009 MAP3K7 0.789 0.003 MGMT 0.632 <.001 0.693<.001 MICA 0.781 0.014 0.653 <.001 0.833 0.043 MPPED2 0.655 <.001 0.597<.001 0.719 <.001 0.759 0.006 MSH6 0.793 0.015 MTSS1 0.613 <.001 0.7460.008 MVP 0.792 0.028 0.795 0.045 0.819 0.023 MYBPC1 0.648 <.001 0.496<.001 0.701 <.001 0.629 <.001 NCAM1 0.773 0.015 NCAPD3 0.574 <.001 0.463<.001 0.679 <.001 0.640 <.001 NEXN 0.701 0.002 0.791 0.035 0.725 0.0020.781 0.016 NFAT5 0.515 <.001 0.586 <.001 0.785 0.017 NFATC2 0.753 0.023NFKBIA 0.778 0.037 NRG1 0.644 0.004 0.696 0.017 0.698 0.012 OAZ1 0.7770.034 0.775 0.022 OLFML3 0.621 <.001 0.720 0.001 0.600 <.001 0.626 <.001OMD 0.706 0.003 OR51E2 0.820 0.037 0.798 0.027 PAGE4 0.549 <.001 0.613<.001 0.542 <.001 0.628 <.001 PCA3 0.684 <.001 0.635 <.001 PCDHGB7 0.7900.045 0.725 0.002 0.664 <.001 PGF 0.753 0.017 PGR 0.740 0.021 0.7280.018 PIK3CG 0.803 0.024 PLAUR 0.778 0.035 PLG 0.728 0.028 PPAP2B 0.575<.001 0.629 <.001 0.643 <.001 0.699 <.001 PPP1R12A 0.647 <.001 0.6830.002 0.782 0.023 0.784 0.030 PRIMA1 0.626 <.001 0.658 <.001 0.703 0.0020.724 0.003 PRKCA 0.642 <.001 0.799 0.029 0.677 0.001 0.776 0.006 PRKCB0.675 0.001 0.648 <.001 0.747 0.006 PROM1 0.603 0.018 0.659 0.014 0.4930.008 PTCH1 0.680 0.001 0.753 0.010 0.789 0.018 PTEN 0.732 0.002 0.7470.005 0.744 <.001 0.765 0.002 PTGS2 0.596 <.001 0.610 <.001 PTH1R 0.7670.042 0.775 0.028 0.788 0.047 PTHLH 0.617 0.002 0.726 0.025 0.668 0.0020.718 0.007 PTK2B 0.744 0.003 0.679 <.001 0.766 0.002 0.726 <.001 PTPN10.760 0.020 0.780 0.042 PYCARD 0.748 0.012 RAB27A 0.708 0.004 RAB300.755 0.008 RAGE 0.817 0.048 RAP1B 0.818 0.050 RARB 0.757 0.007 0.677<.001 0.789 0.007 0.746 0.003 RASSF1 0.816 0.035 RHOB 0.725 0.009 0.6760.001 0.793 0.039 RLN1 0.742 0.033 0.762 0.040 RND3 0.636 <.001 0.647<.001 RNF114 0.749 0.011 SDC2 0.721 0.004 SDHC 0.725 0.003 0.727 0.006SEMA3A 0.757 0.024 0.721 0.010 SERPINA3 0.716 0.008 0.660 0.001 SERPINB50.747 0.031 0.616 0.002 SH3RF2 0.577 <.001 0.458 <.001 0.702 <.001 0.640<.001 SLC22A3 0.565 <.001 0.540 <.001 0.747 0.004 0.756 0.007 SMAD40.546 <.001 0.573 <.001 0.636 <.001 0.627 <.001 SMARCD1 0.718 <.0010.775 0.017 SMO 0.793 0.029 0.754 0.021 0.718 0.003 SOD1 0.757 0.0490.707 0.006 SORBS1 0.645 <.001 0.716 0.003 0.693 <.001 0.784 0.025SPARCL1 0.821 0.028 0.829 0.014 0.781 0.030 SPDEF 0.778 <.001 SPINT10.732 0.009 0.842 0.026 SRC 0.647 <.001 0.632 <.001 SRD5A1 0.813 0.040SRD5A2 0.489 <.001 0.533 <.001 0.544 <.001 0.611 <.001 ST5 0.713 0.0020.783 0.011 0.725 <.001 0.827 0.025 STAT3 0.773 0.037 0.759 0.035 STAT5A0.695 <.001 0.719 0.002 0.806 0.020 0.783 0.008 STAT5B 0.633 <.001 0.655<.001 0.814 0.028 SUMO1 0.790 0.015 SVIL 0.659 <.001 0.713 0.002 0.7110.002 0.779 0.010 TARP 0.800 0.040 TBP 0.761 0.010 TFF3 0.734 0.0100.659 <.001 TGFB1I1 0.618 <.001 0.693 0.002 0.637 <.001 0.719 0.004TGFB2 0.679 <.001 0.747 0.005 0.805 0.030 TGFB3 0.791 0.037 TGFBR2 0.7780.035 TIMP3 0.751 0.011 TMPRSS2 0.745 0.003 0.708 <.001 TNF 0.670 0.0130.697 0.015 TNFRSF10A 0.780 0.018 0.752 0.006 0.817 0.032 TNFRSF10B0.576 <.001 0.655 <.001 0.766 0.004 0.778 0.002 TNFRSF18 0.648 0.0160.759 0.034 TNFSF10 0.653 <.001 0.667 0.004 TP53 0.729 0.003 TP63 0.7590.016 0.636 <.001 0.698 <.001 0.712 0.001 TPM1 0.778 0.048 0.743 0.0120.783 0.032 0.811 0.046 TPM2 0.578 <.001 0.634 <.001 0.611 <.001 0.7100.001 TPP2 0.775 0.037 TRAF3IP2 0.722 0.002 0.690 <.001 0.792 0.0210.823 0.049 TRO 0.744 0.003 0.725 0.003 0.765 0.002 0.821 0.041 TUBB2A0.639 <.001 0.625 <.001 TYMP 0.786 0.039 VCL 0.594 <.001 0.657 0.0010.682 <.001 VEGFA 0.762 0.024 VEGFB 0.795 0.037 VIM 0.739 0.009 0.7910.021 WDR19 0.776 0.015 WFDC1 0.746 <.001 YY1 0.683 0.001 0.728 0.002ZFHX3 0.684 <.001 0.661 <.001 0.801 0.010 0.762 0.001 ZFP36 0.605 <.0010.579 <.001 0.815 0.043 ZNF827 0.624 <.001 0.730 0.007 0.738 0.004

Tables 5A and 5B provide genes that were significantly associated(p<0.05), positively or negatively, with recurrence (cRFI, bRFI) afteradjusting for AUA risk group in the primary and/or highest Gleasonpattern. Increased expression of genes in Table 5A is negativelyassociated with good prognosis, while increased expression of genes inTable 5B is positively associated with good prognosis.

TABLE 5A Gene significantly (p < 0.05) associated with cRFI or bRFIafter adjustment for AUA risk group in the primary Gleason pattern orhighest Gleason pattern with hazard ratio (HR) >1.0 (increasedexpression negatively associated with good prognosis) cRFI cRFI bRFIbRFI Primary Highest Primary Highest Pattern Pattern Pattern PatternOfficial p- p- p- p- Symbol HR value HR value HR value HR value AKR1C31.315 0.018 1.283 0.024 ALOX12 1.198 0.024 ANLN 1.406 <.001 1.519 <.0011.485 <.001 1.632 <.001 AQP2 1.209 <.001 1.302 <.001 ASAP2 1.582 <.0011.333 0.011 1.307 0.019 ASPN 1.872 <.001 1.741 <.001 1.638 <.001 1.691<.001 ATP5E 1.309 0.042 1.369 0.012 BAG5 1.291 0.044 BAX 1.298 0.0251.420 0.004 BGN 1.746 <.001 1.755 <.001 BIRC5 1.480 <.001 1.470 <.0011.419 <.001 1.503 <.001 BMP6 1.536 <.001 1.815 <.001 1.294 0.033 1.4290.001 BRCA2 1.184 0.037 BUB1 1.288 0.001 1.391 <.001 1.254 <.001 1.1890.018 CACNA1D 1.313 0.029 CADPS 1.358 0.007 1.267 0.022 CASP3 1.2510.037 CCNB1 1.261 0.033 1.318 0.005 CCNE2 1.345 0.005 1.438 <.001 1.606<.001 1.426 <.001 CD276 1.482 0.002 1.668 <.001 1.451 <.001 1.302 0.011CDC20 1.417 <.001 1.547 <.001 1.355 <.001 1.446 <.001 CDC6 1.340 0.0111.265 0.046 1.367 0.002 1.272 0.025 CDH7 1.402 0.003 1.409 0.002 CDKN2B1.553 <.001 1.746 <.001 1.340 0.014 1.369 0.006 CDKN2C 1.411 <.001 1.604<.001 1.220 0.033 CDKN3 1.296 0.004 1.226 0.015 CENPF 1.434 0.002 1.570<.001 1.633 <.001 1.610 <.001 CKS2 1.419 0.008 1.374 0.022 1.380 0.004COL1A1 1.677 <.001 1.809 <.001 1.401 <.001 1.352 0.003 COL1A2 1.3730.010 COL3A1 1.669 <.001 1.781 <.001 1.249 0.024 1.234 0.047 COL4A11.475 0.002 1.513 0.002 COL8A1 1.506 0.001 1.691 <.001 CRISP3 1.4060.004 1.471 <.001 CTHRC1 1.426 0.009 1.793 <.001 1.311 0.019 CTNND21.462 <.001 DDIT4 1.478 0.003 1.783 <.001 1.236 0.039 DYNLL1 1.431 0.0021.193 0.004 EIF3H 1.372 0.027 ENY2 1.325 0.023 1.270 0.017 ERG 1.3030.041 EZH2 1.254 0.049 F2R 1.540 0.002 1.448 0.006 1.286 0.023 FADD1.235 0.041 1.404 <.001 FAP 1.386 0.015 1.440 0.008 1.253 0.048 FASN1.303 0.028 FCGR3A 1.439 0.011 1.262 0.045 FGF5 1.289 0.006 GNPTAB 1.2900.033 1.369 0.022 1.285 0.018 1.355 0.008 GPR68 1.396 0.005 GREM1 1.3410.022 1.502 0.003 1.366 0.006 HDAC1 1.329 0.016 HDAC9 1.378 0.012 HRAS1.465 0.006 HSD17B4 1.442 <.001 1.245 0.028 IGFBP3 1.366 0.019 1.3020.011 INHBA 2.000 <.001 2.336 <.001 1.486 0.002 JAG1 1.251 0.039 KCNN21.347 0.020 1.524 <.001 1.312 0.023 1.346 0.011 KHDRBS3 1.500 0.0011.426 0.001 1.267 0.032 KIAA0196 1.272 0.028 KIF4A 1.199 0.022 1.2620.004 KPNA2 1.252 0.016 LAMA3 1.332 0.004 1.356 0.010 LAMB1 1.317 0.028LAMC1 1.516 0.003 1.302 0.040 1.397 0.007 LIMS1 1.261 0.027 LOX 1.2650.016 1.372 0.001 LTBP2 1.477 0.002 LUM 1.321 0.020 MANF 1.647 <.0011.284 0.027 MCM2 1.372 0.003 1.302 0.032 MCM3 1.269 0.047 MCM6 1.2760.033 1.245 0.037 MELK 1.294 0.005 1.394 <.001 MKI67 1.253 0.028 1.2460.029 MMP11 1.557 <.001 1.290 0.035 1.357 0.005 MRPL13 1.275 0.003 MSH21.355 0.009 MYBL2 1.497 <.001 1.509 <.001 1.304 0.003 1.292 0.007 MYO61.367 0.010 NDRG1 1.270 0.042 1.314 0.025 NEK2 1.338 0.020 1.269 0.026NETO2 1.434 0.004 1.303 0.033 1.283 0.012 NOX4 1.413 0.006 1.308 0.0371.444 <.001 NRIP3 1.171 0.026 NRP1 1.372 0.020 ODC1 1.450 <.001 OR51E11.559 <.001 1.413 0.008 PAK6 1.233 0.047 PATE1 1.262 <.001 1.375 <.0011.143 0.034 1.191 0.036 PCNA 1.227 0.033 1.318 0.003 PEX10 1.517 <.0011.500 0.001 PGD 1.363 0.028 1.316 0.039 1.652 <.001 PGK1 1.224 0.0341.206 0.024 PIM1 1.205 0.042 PLA2G7 1.298 0.018 1.358 0.005 PLAU 1.2420.032 PLK1 1.464 0.001 1.299 0.018 1.275 0.031 PLOD2 1.206 0.039 1.2610.025 POSTN 1.558 0.001 1.356 0.022 1.363 0.009 PPP3CA 1.445 0.002PSMD13 1.301 0.017 1.411 0.003 PTK2 1.318 0.031 PTK6 1.582 <.001 1.894<.001 1.290 0.011 1.354 0.003 PTTG1 1.319 0.004 1.430 <.001 1.271 0.0061.492 <.001 RAD21 1.278 0.028 1.435 0.004 1.326 0.008 RAF1 1.504 <.001RALA 1.374 0.028 1.459 0.001 RGS7 1.203 0.031 RRM1 1.535 0.001 1.525<.001 RRM2 1.302 0.003 1.197 0.047 1.342 <.001 SAT1 1.374 0.043 SDC11.344 0.011 1.473 0.008 SEC14L1 1.297 0.006 SESN3 1.337 0.002 1.495<.001 1.223 0.038 SFRP4 1.610 <.001 1.542 0.002 1.370 0.009 SHMT2 1.5670.001 1.522 <.001 1.485 0.001 1.370 <.001 SKIL 1.303 0.008 SLC25A211.287 0.020 1.306 0.017 SLC44A1 1.308 0.045 SNRPB2 1.304 0.018 SOX41.252 0.031 SPARC 1.445 0.004 1.706 <.001 1.269 0.026 SPP1 1.376 0.016SQLE 1.417 0.007 1.262 0.035 STAT1 1.209 0.029 STMN1 1.315 0.029 SULF11.504 0.001 TAF2 1.252 0.048 1.301 0.019 TFDP1 1.395 0.010 1.424 0.002THBS2 1.716 <.001 1.719 <.001 THY1 1.343 0.035 1.575 0.001 TK1 1.320<.001 1.304 <.001 TOP2A 1.464 0.001 1.688 <.001 1.715 <.001 1.761 <.001TPD52 1.286 0.006 1.258 0.023 TPX2 1.644 <.001 1.964 <.001 1.699 <.0011.754 <.001 TYMS 1.315 0.014 UBE2C 1.270 0.019 1.558 <.001 1.205 0.0271.333 <.001 UBE2G1 1.302 0.041 UBE2T 1.451 <.001 1.309 0.003 UGT2B151.222 0.025 UHRF1 1.370 0.003 1.520 <.001 1.247 0.020 VCPIP1 1.332 0.015VTI1B 1.237 0.036 XIAP 1.486 0.008 ZMYND8 1.408 0.007 ZNF3 1.284 0.018ZWINT 1.289 0.028

TABLE 5B Genes significantly (p < 0.05) associated with cRFI or bRFIafter adjustment for AUA risk group in the primary Gleason pattern orhighest Gleason pattern with hazard ratio (HR) <1.0 (increasedexpression is positively associated with good prognosis) cRFI cRFI bRFIbRFI Primary Highest Primary Highest Pattern Pattern Pattern PatternOfficial p- p- p- p- Symbol HR value HR value HR value HR value AAMP0.535 <.001 0.581 <.001 0.700 0.002 0.759 0.006 ABCA5 0.798 0.007 0.7450.002 0.841 0.037 ABCC1 0.800 0.044 ABCC4 0.787 0.022 ABHD2 0.768 0.023ACOX2 0.678 0.002 0.749 0.027 0.759 0.004 ADH5 0.645 <.001 0.672 0.001AGTR1 0.780 0.030 AKAP1 0.815 0.045 0.758 <.001 AKT1 0.732 0.010 ALDH1A20.646 <.001 0.548 <.001 0.671 <.001 0.713 0.001 ANPEP 0.641 <.001 0.535<.001 ANXA2 0.772 0.035 0.804 0.046 ATXN1 0.654 <.001 0.754 0.020 0.7970.017 AURKA 0.788 0.030 AXIN2 0.744 0.005 0.655 <.001 AZGP1 0.656 <.0010.676 <.001 0.754 0.001 0.791 0.004 BAD 0.700 0.004 BIN1 0.650 <.0010.764 0.013 0.803 0.015 BTG3 0.836 0.025 BTRC 0.730 0.005 C7 0.617 <.0010.680 <.001 0.667 <.001 0.755 0.005 CADM1 0.559 <.001 0.566 <.001 0.7720.020 0.802 0.046 CASP1 0.781 0.030 0.779 0.021 0.818 0.027 0.828 0.036CAV1 0.775 0.034 CAV2 0.677 0.019 CCL2 0.752 0.023 CCNH 0.679 <.0010.682 <.001 CD164 0.721 0.002 0.724 0.005 CD1A 0.710 0.014 CD44 0.591<.001 0.642 <.001 CD82 0.779 0.021 0.771 0.024 CDC25B 0.778 0.035 0.8180.023 CDK14 0.788 0.011 CDK3 0.752 0.012 0.779 0.005 0.841 0.020 CDKN1A0.770 0.049 0.712 0.014 CDKN1C 0.684 <.001 0.697 <.001 CHN1 0.772 0.031COL6A1 0.648 <.001 0.807 0.046 0.768 0.004 CSF1 0.621 <.001 0.671 0.001CTNNB1 0.905 0.008 CTSB 0.754 0.030 0.716 0.011 0.756 0.014 CXCL12 0.641<.001 0.796 0.038 0.708 <.001 CYP3A5 0.503 <.001 0.528 <.001 0.791 0.028CYR61 0.639 0.001 0.659 0.001 0.797 0.048 DARC 0.707 0.004 DDR2 0.7500.011 DES 0.657 <.001 0.758 0.022 0.699 <.001 DHRS9 0.625 0.002 DHX90.846 <.001 DIAPH1 0.682 0.007 0.723 0.008 0.780 0.026 DLC1 0.703 0.0050.702 0.008 DLGAP1 0.703 0.008 0.636 <.001 DNM3 0.701 0.001 0.817 0.042DPP4 0.686 <.001 0.716 0.001 DPT 0.636 <.001 0.633 <.001 0.709 0.0060.773 0.024 DUSP1 0.683 0.006 0.679 0.003 DUSP6 0.694 0.003 0.605 <.001EDN1 0.773 0.031 EDNRA 0.716 0.007 EGR1 0.575 <.001 0.575 <.001 0.7710.014 EGR3 0.633 0.002 0.643 <.001 0.792 0.025 EIF4E 0.722 0.002 ELK40.710 0.009 0.759 0.027 ENPP2 0.786 0.039 EPHA2 0.593 0.001 EPHA3 0.7390.006 0.802 0.020 ERBB2 0.753 0.007 ERBB3 0.753 0.009 0.753 0.015 ERCC10.727 0.001 EREG 0.722 0.012 0.769 0.040 ESR1 0.742 0.015 FABP5 0.7560.032 FAM107A 0.524 <.001 0.579 <.001 0.688 <.001 0.699 0.001 FAM13C0.639 <.001 0.601 <.001 0.810 0.019 0.709 <.001 FAS 0.770 0.033 FASLG0.716 0.028 0.683 0.017 FGF10 0.798 0.045 FGF17 0.718 0.018 0.793 0.0240.790 0.024 FGFR2 0.739 0.007 0.783 0.038 0.740 0.004 FGFR4 0.746 0.050FKBP5 0.689 0.003 FLNA 0.701 0.006 0.766 0.029 0.768 0.037 FLNC 0.755<.001 0.820 0.022 FLT1 0.729 0.008 FOS 0.572 <.001 0.536 <.001 0.7500.005 FOXQ1 0.778 0.033 0.820 0.018 FYN 0.708 0.006 GADD45B 0.577 <.0010.589 <.001 GDF15 0.757 0.013 0.743 0.006 GHR 0.712 0.004 0.679 0.001GNRH1 0.791 0.048 GPM6B 0.675 <.001 0.660 <.001 0.735 <.001 0.823 0.049GSK3B 0.783 0.042 GSN 0.587 <.001 0.705 0.002 0.745 0.004 0.796 0.021GSTM1 0.686 0.001 0.631 <.001 0.807 0.018 GSTM2 0.607 <.001 0.683 <.0010.679 <.001 0.800 0.027 HIRIP3 0.692 <.001 0.782 0.007 HK1 0.724 0.0020.718 0.002 HLF 0.580 <.001 0.571 <.001 0.759 0.008 0.750 0.004 HNF1B0.669 <.001 HPS1 0.764 0.008 HSD17B10 0.802 0.045 HSD17B2 0.723 0.048HSD3B2 0.709 0.010 HSP90AB1 0.780 0.034 0.809 0.041 HSPA5 0.738 0.017HSPB1 0.770 0.006 0.801 0.032 HSPB2 0.788 0.035 ICAM1 0.728 0.015 0.7160.010 IER3 0.735 0.016 0.637 <.001 0.802 0.035 IFIT1 0.647 <.001 0.7550.029 IGF1 0.675 <.001 0.603 <.001 0.762 0.006 0.770 0.030 IGF2 0.7610.011 IGFBP2 0.601 <.001 0.605 <.001 IGFBP5 0.702 <.001 IGFBP6 0.628<.001 0.726 0.003 IL1B 0.676 0.002 0.716 0.004 IL6 0.688 0.005 0.7660.044 IL6R 0.786 0.036 IL6ST 0.618 <.001 0.639 <.001 0.785 0.027 0.8130.042 IL8 0.635 <.001 0.628 <.001 ILK 0.734 0.018 0.753 0.026 ING5 0.684<.001 0.681 <.001 0.756 0.006 ITGA4 0.778 0.040 ITGA5 0.762 0.026 ITGA60.811 0.038 ITGA7 0.592 <.001 0.715 0.006 0.710 0.002 ITGAD 0.576 0.006ITGB4 0.693 0.003 ITPR1 0.789 0.029 JUN 0.572 <.001 0.581 <.001 0.7770.019 JUNB 0.732 0.030 0.707 0.016 KCTD12 0.758 0.036 KIT 0.691 0.0090.738 0.028 KLC1 0.741 0.024 0.781 0.024 KLF6 0.733 0.018 0.727 0.014KLK1 0.744 0.028 KLK2 0.697 0.002 0.679 <.001 KLK3 0.725 <.001 0.715<.001 0.841 0.023 KRT15 0.660 <.001 0.577 <.001 0.750 0.002 KRT18 0.623<.001 0.642 <.001 0.702 <.001 0.760 0.006 KRT2 0.740 0.044 KRT5 0.674<.001 0.588 <.001 0.769 0.005 KRT8 0.768 0.034 L1CAM 0.737 0.036 LAG30.711 0.013 0.748 0.029 LAMA4 0.649 0.009 LAMB3 0.709 0.002 0.684 0.0060.768 0.006 LGALS3 0.652 <.001 0.752 0.015 0.805 0.028 LIG3 0.728 0.0160.667 <.001 LRP1 0.811 0.043 MDM2 0.788 0.033 MGMT 0.645 <.001 0.7660.015 MICA 0.796 0.043 0.676 <.001 MPPED2 0.675 <.001 0.616 <.001 0.7500.006 MRC1 0.788 0.028 MTSS1 0.654 <.001 0.793 0.036 MYBPC1 0.706 <.0010.534 <.001 0.773 0.004 0.692 <.001 NCAPD3 0.658 <.001 0.566 <.001 0.7530.011 0.733 0.009 NCOR1 0.838 0.045 NEXN 0.748 0.025 0.785 0.020 NFAT50.531 <.001 0.626 <.001 NFATC2 0.759 0.024 OAZ1 0.766 0.024 OLFML3 0.648<.001 0.748 0.005 0.639 <.001 0.675 <.001 OR51E2 0.823 0.034 PAGE4 0.599<.001 0.698 0.002 0.606 <.001 0.726 <.001 PCA3 0.705 <.001 0.647 <.001PCDHGB7 0.712 <.001 PGF 0.790 0.039 PLG 0.764 0.048 PLP2 0.766 0.037PPAP2B 0.589 <.001 0.647 <.001 0.691 <.001 0.765 0.013 PPP1R12A 0.6730.001 0.677 0.001 0.807 0.045 PRIMA1 0.622 <.001 0.712 0.008 0.740 0.013PRKCA 0.637 <.001 0.694 <.001 PRKCB 0.741 0.020 0.664 <.001 PROM1 0.5990.017 0.527 0.042 0.610 0.006 0.420 0.002 PTCH1 0.752 0.027 0.762 0.011PTEN 0.779 0.011 0.802 0.030 0.788 0.009 PTGS2 0.639 <.001 0.606 <.001PTHLH 0.632 0.007 0.739 0.043 0.654 0.002 0.740 0.015 PTK2B 0.775 0.0190.831 0.028 0.810 0.017 PTPN1 0.721 0.012 0.737 0.024 PYCARD 0.702 0.005RAB27A 0.736 0.008 RAB30 0.761 0.011 RARB 0.746 0.010 RASSF1 0.805 0.043RHOB 0.755 0.029 0.672 0.001 RLN1 0.742 0.036 0.740 0.036 RND3 0.607<.001 0.633 <.001 RNF114 0.782 0.041 0.747 0.013 SDC2 0.714 0.002 SDHC0.698 <.001 0.762 0.029 SERPINA3 0.752 0.030 SERPINB5 0.669 0.014 SH3RF20.705 0.012 0.568 <.001 0.755 0.016 SLC22A3 0.650 <.001 0.582 <.001SMAD4 0.636 <.001 0.684 0.002 0.741 0.007 0.738 0.007 SMARCD1 0.7570.001 SMO 0.790 0.049 0.766 0.013 SOD1 0.741 0.037 0.713 0.007 SORBS10.684 0.003 0.732 0.008 0.788 0.049 SPDEF 0.840 0.012 SPINT1 0.837 0.048SRC 0.674 <.001 0.671 <.001 SRD5A2 0.553 <.001 0.588 <.001 0.618 <.0010.701 <.001 ST5 0.747 0.012 0.761 0.010 0.780 0.016 0.832 0.041 STAT30.735 0.020 STAT5A 0.731 0.005 0.743 0.009 0.817 0.027 STAT5B 0.708<.001 0.696 0.001 SUMO1 0.815 0.037 SVIL 0.689 0.003 0.739 0.008 0.7610.011 TBP 0.792 0.037 TFF3 0.719 0.007 0.664 0.001 TGFB1I1 0.676 0.0030.707 0.007 0.709 0.005 0.777 0.035 TGFB2 0.741 0.010 0.785 0.017 TGFBR20.759 0.022 TIMP3 0.785 0.037 TMPRSS2 0.780 0.012 0.742 <.001 TNF 0.6540.007 0.682 0.006 TNFRSF10B 0.623 <.001 0.681 <.001 0.801 0.018 0.8150.019 TNFSF10 0.721 0.004 TP53 0.759 0.011 TP63 0.737 0.020 0.754 0.007TPM2 0.609 <.001 0.671 <.001 0.673 <.001 0.789 0.031 TRAF3IP2 0.7950.041 0.727 0.005 TRO 0.793 0.033 0.768 0.027 0.814 0.023 TUBB2A 0.626<.001 0.590 <.001 VCL 0.613 <.001 0.701 0.011 VIM 0.716 0.005 0.7920.025 WFDC1 0.824 0.029 YY1 0.668 <.001 0.787 0.014 0.716 0.001 0.8190.011 ZFHX3 0.732 <.001 0.709 <.001 ZFP36 0.656 0.001 0.609 <.001 0.8180.045 ZNF827 0.750 0.022

Tables 6A and 6B provide genes that were significantly associated(p<0.05), positively or negatively, with recurrence (cRFI, bRFI) afteradjusting for Gleason pattern in the primary and/or highest Gleasonpattern. Increased expression of genes in Table 6A is negativelyassociated with good prognosis, while increased expression of gene inTable 6B is positively associated with good prognosis.

TABLE 6A Genes significantly (p < 0.05) associated with cRFI or bRFIafter adjustment for Gleason pattern in the primary Gleason pattern orhighest Gleason pattern with a hazard ratio (HR) >1.0 (increasedexpression is negatively associated with good prognosis) cRFI cRFI bRFIbRFI Primary Highest Primary Highest Pattern Pattern Pattern PatternOfficial p- p- p- p- Symbol HR value HR value HR value HR value AKR1C31.258 0.039 ANLN 1.292 0.023 1.449 <.001 1.420 0.001 AQP2 1.178 0.0081.287 <.001 ASAP2 1.396 0.015 ASPN 1.809 <.001 1.508 0.009 1.506 0.0021.438 0.002 BAG5 1.367 0.012 BAX 1.234 0.044 BGN 1.465 0.009 1.342 0.046BIRC5 1.338 0.008 1.364 0.004 1.279 0.006 BMP6 1.369 0.015 1.518 0.002BUB1 1.239 0.024 1.227 0.001 1.236 0.004 CACNA1D 1.337 0.025 CADPS 1.2800.029 CCNE2 1.256 0.043 1.577 <.001 1.324 0.001 CD276 1.320 0.029 1.3960.007 1.279 0.033 CDC20 1.298 0.016 1.334 0.002 1.257 0.032 1.279 0.003CDH7 1.258 0.047 1.338 0.013 CDKN2B 1.342 0.032 1.488 0.009 CDKN2C 1.3440.010 1.450 <.001 CDKN3 1.284 0.012 CENPF 1.289 0.048 1.498 0.001 1.3440.010 COL1A1 1.481 0.003 1.506 0.002 COL3A1 1.459 0.004 1.430 0.013COL4A1 1.396 0.015 COL8A1 1.413 0.008 CRISP3 1.346 0.012 1.310 0.025CTHRC1 1.588 0.002 DDIT4 1.363 0.020 1.379 0.028 DICER1 1.294 0.008 ENY21.269 0.024 FADD 1.307 0.010 FAS 1.243 0.025 FGF5 1.328 0.002 GNPTAB1.246 0.037 GREM1 1.332 0.024 1.377 0.013 1.373 0.011 HDAC1 1.301 0.0181.237 0.021 HSD17B4 1.277 0.011 IFN-γ 1.219 0.048 IMMT 1.230 0.049 INHBA1.866 <.001 1.944 <.001 JAG1 1.298 0.030 KCNN2 1.378 0.020 1.282 0.017KHDRBS3 1.353 0.029 1.305 0.014 LAMA3 1.344 <.001 1.232 0.048 LAMC11.396 0.015 LIMS1 1.337 0.004 LOX 1.355 0.001 1.341 0.002 LTBP2 1.3040.045 MAGEA4 1.215 0.024 MANF 1.460 <.001 MCM6 1.287 0.042 1.214 0.046MELK 1.329 0.002 MMP11 1.281 0.050 MRPL13 1.266 0.021 MYBL2 1.453 <.0011.274 0.019 MYC 1.265 0.037 MYO6 1.278 0.047 NETO2 1.322 0.022 NFKB11.255 0.032 NOX4 1.266 0.041 OR51E1 1.566 <.001 1.428 0.003 PATE1 1.242<.001 1.347 <.001 1.177 0.011 PCNA 1.251 0.025 PEX10 1.302 0.028 PGD1.335 0.045 1.379 0.014 1.274 0.025 PIM1 1.254 0.019 PLA2G7 1.289 0.0251.250 0.031 PLAU 1.267 0.031 PSMD13 1.333 0.005 PTK6 1.432 <.001 1.577<.001 1.223 0.040 PTTG1 1.279 0.013 1.308 0.006 RAGE 1.329 0.011 RALA1.363 0.044 1.471 0.003 RGS7 1.120 0.040 1.173 0.031 RRM1 1.490 0.0041.527 <.001 SESN3 1.353 0.017 SFRP4 1.370 0.025 SHMT2 1.460 0.008 1.4100.006 1.407 0.008 1.345 <.001 SKIL 1.307 0.025 SLC25A21 1.414 0.0021.330 0.004 SMARCC2 1.219 0.049 SPARC 1.431 0.005 TFDP1 1.283 0.0461.345 0.003 THBS2 1.456 0.005 1.431 0.012 TK1 1.214 0.015 1.222 0.006TOP2A 1.367 0.018 1.518 0.001 1.480 <.001 TPX2 1.513 0.001 1.607 <.0011.588 <.001 1.481 <.001 UBE2T 1.409 0.002 1.285 0.018 UGT2B15 1.2160.009 1.182 0.021 XIAP 1.336 0.037 1.194 0.043

TABLE 6B Genes significantly (p < 0.05) associated with cRFI or bRFIafter adjustment for Gleason pattern in the primary Gleason pattern orhighest Gleason pattern with hazard ration (HR) <1.0 (increasedexpression is positively associated with good prognosis) cRFI cRFI bRFIbRFI Primary Highest Primary Highest Pattern Pattern Pattern PatternOfficial p- p- p- p- Symbol HR value HR value HR value HR value AAMP0.660 0.001 0.675 <.001 0.836 0.045 ABCA5 0.807 0.014 0.737 <.001 0.8450.030 ABCC1 0.780 0.038 0.794 0.015 ABCG2 0.807 0.035 ABHD2 0.720 0.002ADH5 0.750 0.034 AKAP1 0.721 <.001 ALDH1A2 0.735 0.009 0.592 <.001 0.7560.007 0.781 0.021 ANGPT2 0.741 0.036 ANPEP 0.637 <.001 0.536 <.001 ANXA20.762 0.044 APOE 0.707 0.013 APRT 0.727 0.004 0.771 0.006 ATXN1 0.7250.013 AURKA 0.784 0.037 0.735 0.003 AXIN2 0.744 0.004 0.630 <.001 AZGP10.672 <.001 0.720 <.001 0.764 0.001 BAD 0.687 <.001 BAK1 0.783 0.014BCL2 0.777 0.033 0.772 0.036 BIK 0.768 0.040 BIN1 0.691 <.001 BTRC 0.7760.029 C7 0.707 0.004 0.791 0.024 CADM1 0.587 <.001 0.593 <.001 CASP10.773 0.023 0.820 0.025 CAV1 0.753 0.014 CAV2 0.627 0.009 0.682 0.003CCL2 0.740 0.019 CCNH 0.736 0.003 CCR1 0.755 0.022 CD1A 0.740 0.025 CD440.590 <.001 0.637 <.001 CD68 0.757 0.026 CD82 0.778 0.012 0.759 0.016CDC25B 0.760 0.021 CDK3 0.762 0.024 0.774 0.007 CDKN1A 0.714 0.015CDKN1C 0.738 0.014 0.768 0.021 COL6A1 0.690 <.001 0.805 0.048 CSF1 0.6750.002 0.779 0.036 CSK 0.825 0.004 CTNNB1 0.884 0.045 0.888 0.027 CTSB0.740 0.017 0.676 0.003 0.755 0.010 CTSD 0.673 0.031 0.722 0.009 CTSK0.804 0.034 CTSL2 0.748 0.019 CXCL12 0.731 0.017 CYP3A5 0.523 <.0010.518 <.001 CYR61 0.744 0.041 DAP 0.755 0.011 DARC 0.763 0.029 DDR20.813 0.041 DES 0.743 0.020 DHRS9 0.606 0.001 DHX9 0.916 0.021 DIAPH10.749 0.036 0.688 0.003 DLGAP1 0.758 0.042 0.676 0.002 DLL4 0.779 0.010DNM3 0.732 0.007 DPP4 0.732 0.004 0.750 0.014 DPT 0.704 0.014 DUSP60.662 <.001 0.665 0.001 EBNA1BP2 0.828 0.019 EDNRA 0.782 0.048 EGF 0.7120.023 EGR1 0.678 0.004 0.725 0.028 EGR3 0.680 0.006 0.738 0.027 EIF2C20.789 0.032 EIF2S3 0.759 0.012 ELK4 0.745 0.024 EPHA2 0.661 0.007 EPHA30.781 0.026 0.828 0.037 ERBB2 0.791 0.022 0.760 0.014 0.789 0.006 ERBB30.757 0.009 ERCC1 0.760 0.008 ESR1 0.742 0.014 ESR2 0.711 0.038 ETV40.714 0.035 FAM107A 0.619 <.001 0.710 0.011 0.781 0.019 FAM13C 0.664<.001 0.686 <.001 0.813 0.014 FAM49B 0.670 <.001 0.793 0.014 0.815 0.0440.843 0.047 FASLG 0.616 0.004 0.813 0.038 FGF10 0.751 0.028 0.766 0.019FGF17 0.718 0.031 0.765 0.019 FGFR2 0.740 0.009 0.738 0.002 FKBP5 0.7490.031 FLNC 0.826 0.029 FLT1 0.779 0.045 0.729 0.006 FLT4 0.815 0.024 FOS0.657 0.003 0.656 0.004 FSD1 0.763 0.017 FYN 0.716 0.004 0.792 0.024GADD45B 0.692 0.009 0.697 0.010 GDF15 0.767 0.016 GHR 0.701 0.002 0.7040.002 0.640 <.001 GNRH1 0.778 0.039 GPM6B 0.749 0.010 0.750 0.010 0.8270.037 GRB7 0.696 0.005 GSK3B 0.726 0.005 GSN 0.660 <.001 0.752 0.019GSTM1 0.710 0.004 0.676 <.001 GSTM2 0.643 <.001 0.767 0.015 HK1 0.7980.035 HLA-G 0.660 0.013 HLF 0.644 <.001 0.727 0.011 HNF1B 0.755 0.013HPS1 0.756 0.006 0.791 0.043 HSD17B10 0.737 0.006 HSD3B2 0.674 0.003HSP90AB1 0.763 0.015 HSPB1 0.787 0.020 0.778 0.015 HSPE1 0.794 0.039ICAM1 0.664 0.003 IER3 0.699 0.003 0.693 0.010 IFIT1 0.621 <.001 0.7330.027 IGF1 0.751 0.017 0.655 <.001 IGFBP2 0.599 <.001 0.605 <.001 IGFBP50.745 0.007 0.775 0.035 IGFBP6 0.671 0.005 IL1B 0.732 0.016 0.717 0.005IL6 0.763 0.040 IL6R 0.764 0.022 IL6ST 0.647 <.001 0.739 0.012 IL8 0.7110.015 0.694 0.006 ING5 0.729 0.007 0.727 0.003 ITGA4 0.755 0.009 ITGA50.743 0.018 0.770 0.034 ITGA6 0.816 0.044 0.772 0.006 ITGA7 0.680 0.004ITGAD 0.590 0.009 ITGB4 0.663 <.001 0.658 <.001 0.759 0.004 JUN 0.6560.004 0.639 0.003 KIAA0196 0.737 0.011 KIT 0.730 0.021 0.724 0.008 KLC10.755 0.035 KLK1 0.706 0.008 KLK2 0.740 0.016 0.723 0.001 KLK3 0.7650.006 0.740 0.002 KRT1 0.774 0.042 KRT15 0.658 <.001 0.632 <.001 0.7640.008 KRT18 0.703 0.004 0.672 <.001 0.779 0.015 0.811 0.032 KRT5 0.686<.001 0.629 <.001 0.802 0.023 KRT8 0.763 0.034 0.771 0.022 L1CAM 0.7480.041 LAG3 0.693 0.008 0.724 0.020 LAMA4 0.689 0.039 LAMB3 0.667 <.0010.645 <.001 0.773 0.006 LGALS3 0.666 <.001 0.822 0.047 LIG3 0.723 0.008LRP1 0.777 0.041 0.769 0.007 MDM2 0.688 <.001 MET 0.709 0.010 0.7360.028 0.715 0.003 MGMT 0.751 0.031 MICA 0.705 0.002 MPPED2 0.690 0.0010.657 <.001 0.708 <.001 MRC1 0.812 0.049 MSH6 0.860 0.049 MTSS1 0.6860.001 MVP 0.798 0.034 0.761 0.033 MYBPC1 0.754 0.009 0.615 <.001 NCAPD30.739 0.021 0.664 0.005 NEXN 0.798 0.037 NFAT5 0.596 <.001 0.732 0.005NFATC2 0.743 0.016 0.792 0.047 NOS3 0.730 0.012 0.757 0.032 OAZ1 0.7320.020 0.705 0.002 OCLN 0.746 0.043 0.784 0.025 OLFML3 0.711 0.002 0.709<.001 0.720 0.001 OMD 0.729 0.011 0.762 0.033 OSM 0.813 0.028 PAGE40.668 0.003 0.725 0.004 0.688 <.001 0.766 0.005 PCA3 0.736 0.001 0.691<.001 PCDHGB7 0.769 0.019 0.789 0.022 PIK3CA 0.768 0.010 PIK3CG 0.7920.019 0.758 0.009 PLG 0.682 0.009 PPAP2B 0.688 0.005 0.815 0.046PPP1R12A 0.731 0.026 0.775 0.042 PRIMA1 0.697 0.004 0.757 0.032 PRKCA0.743 0.019 PRKCB 0.756 0.036 0.767 0.029 PROM1 0.640 0.027 0.699 0.0340.503 0.013 PTCH1 0.730 0.018 PTEN 0.779 0.015 0.789 0.007 PTGS2 0.644<.001 0.703 0.007 PTHLH 0.655 0.012 0.706 0.038 0.634 0.001 0.665 0.003PTK2B 0.779 0.023 0.702 0.002 0.806 0.015 0.806 0.024 PYCARD 0.659 0.001RAB30 0.779 0.033 0.754 0.014 RARB 0.787 0.043 0.742 0.009 RASSF1 0.7540.005 RHOA 0.796 0.041 0.819 0.048 RND3 0.721 0.011 0.743 0.028 SDC10.707 0.011 SDC2 0.745 0.002 SDHC 0.750 0.013 SERPINA3 0.730 0.016SERPINB5 0.715 0.041 SH3RF2 0.698 0.025 SIPA1L1 0.796 0.014 0.820 0.004SLC22A3 0.724 0.014 0.700 0.008 SMAD4 0.668 0.002 0.771 0.016 SMARCD10.726 <.001 0.700 0.001 0.812 0.028 SMO 0.785 0.027 SOD1 0.735 0.012SORBS1 0.785 0.039 SPDEF 0.818 0.002 SPINT1 0.761 0.024 0.773 0.006 SRC0.709 <.001 0.690 <.001 SRD5A1 0.746 0.010 0.767 0.024 0.745 0.003SRD5A2 0.575 <.001 0.669 0.001 0.674 <.001 0.781 0.018 ST5 0.774 0.027STAT1 0.694 0.004 STAT5A 0.719 0.004 0.765 0.006 0.834 0.049 STAT5B0.704 0.001 0.744 0.012 SUMO1 0.777 0.014 SVIL 0.771 0.026 TBP 0.7740.031 TFF3 0.742 0.015 0.719 0.024 TGFB1I1 0.763 0.048 TGFB2 0.729 0.0110.758 0.002 TMPRSS2 0.810 0.034 0.692 <.001 TNF 0.727 0.022 TNFRSF10A0.805 0.025 TNFRSF10B 0.581 <.001 0.738 0.014 0.809 0.034 TNFSF10 0.7510.015 0.700 <.001 TP63 0.723 0.018 0.736 0.003 TPM2 0.708 0.010 0.7340.014 TRAF3IP2 0.718 0.004 TRO 0.742 0.012 TSTA3 0.774 0.028 TUBB2A0.659 <.001 0.650 <.001 TYMP 0.695 0.002 VCL 0.683 0.008 VIM 0.778 0.040WDR19 0.775 0.014 XRCC5 0.793 0.042 YY1 0.751 0.025 0.810 0.008 ZFHX30.760 0.005 0.726 0.001 ZFP36 0.707 0.008 0.672 0.003 ZNF827 0.667 0.0020.792 0.039

Tables 7A and 7B provide genes significantly associated (p<0.05),positively or negatively, with clinical recurrence (cRFI) in negativeTMPRSS fusion specimens in the primary or highest Gleason patternspecimen. Increased expression of genes in Table 7A is negativelyassociated with good prognosis, while increased expression of genes inTable 7B is positively associated with good prognosis.

TABLE 7A Genes significantly (p < 0.05) associated with cRFI forTMPRSS2-ERG fusion negative in the primary Gleason pattern or highestGleason pattern with hazard ratio (HR) >1.0 (increased expression isnegatively associated with good prognosis) Official Primary PatternHighest Pattern Symbol HR p-value HR p-value ANLN 1.42 0.012 1.36 0.004AQP2 1.25 0.033 ASPN 2.48 <.001 1.65 <.001 BGN 2.04 <.001 1.45 0.007BIRC5 1.59 <.001 1.37 0.005 BMP6 1.95 <.001 1.43 0.012 BMPR1B 1.93 0.002BUB1 1.51 <.001 1.35 <.001 CCNE2 1.48 0.007 CD276 1.93 <.001 1.79 <.001CDC20 1.49 0.004 1.47 <.001 CDC6 1.52 0.009 1.34 0.022 CDKN2B 1.54 0.0081.55 0.003 CDKN2C 1.55 0.003 1.57 <.001 CDKN3 1.34 0.026 CENPF 1.630.002 1.33 0.018 CKS2 1.50 0.026 1.43 0.009 CLTC 1.46 0.014 COL1A1 1.98<.001 1.50 0.002 COL3A1 2.03 <.001 1.42 0.007 COL4A1 1.81 0.002 COL8A11.63 0.004 1.60 0.001 CRISP3 1.31 0.016 CTHRC1 1.67 0.006 1.48 0.005DDIT4 1.49 0.037 ENY2 1.29 0.039 EZH2 1.35 0.016 F2R 1.46 0.034 1.460.007 FAP 1.66 0.006 1.38 0.012 FGF5 1.46 0.001 GNPTAB 1.49 0.013HSD17B4 1.34 0.039 1.44 0.002 INHBA 2.92 <.001 2.19 <.001 JAG1 1.380.042 KCNN2 1.71 0.002 1.73 <.001 KHDRBS3 1.46 0.015 KLK14 1.28 0.034KPNA2 1.63 0.016 LAMC1 1.41 0.044 LOX 1.29 0.036 LTBP2 1.57 0.017 MELK1.38 0.029 MMP11 1.69 0.002 1.42 0.004 MYBL2 1.78 <.001 1.49 <.001 NETO22.01 <.001 1.43 0.007 NME1 1.38 0.017 PATE1 1.43 <.001 1.24 0.005 PEX101.46 0.030 PGD 1.77 0.002 POSTN 1.49 0.037 1.34 0.026 PPFIA3 1.51 0.012PPP3CA 1.46 0.033 1.34 0.020 PTK6 1.69 <.001 1.56 <.001 PTTG1 1.35 0.028RAD51 1.32 0.048 RALBP1 1.29 0.042 RGS7 1.18 0.012 1.32 0.009 RRM1 1.570.016 1.32 0.041 RRM2 1.30 0.039 SAT1 1.61 0.007 SESN3 1.76 <.001 1.360.020 SFRP4 1.55 0.016 1.48 0.002 SHMT2 2.23 <.001 1.59 <.001 SPARC 1.540.014 SQLE 1.86 0.003 STMN1 2.14 <.001 THBS2 1.79 <.001 1.43 0.009 TK11.30 0.026 TOP2A 2.03 <.001 1.47 0.003 TPD52 1.63 0.003 TPX2 2.11 <.0011.63 <.001 TRAP1 1.46 0.023 UBE2C 1.57 <.001 1.58 <.001 UBE2G1 1.560.008 UBE2T 1.75 <.001 UGT2B15 1.31 0.036 1.33 0.004 UHRF1 1.46 0.007UTP23 1.52 0.017

TABLE 7B Genes significantly (p < 0.05) associated with cRFI forTMPRSS2-ERG fusion negative in the primary Gleason pattern or highestGleason pattern with hazard ratio (HR) <1.0 (increased expression ispositively associated with good prognosis) Official Primary PatternHighest Pattern Symbol HR p-value HR p-value AAMP 0.56 <.001 0.65 0.001ABCA5 0.64 <.001 0.71 <.001 ABCB1 0.62 0.004 ABCC3 0.74 0.031 ABCG2 0.780.050 ABHD2 0.71 0.035 ACOX2 0.54 <.001 0.71 0.007 ADH5 0.49 <.001 0.61<.001 AKAP1 0.77 0.031 0.76 0.013 AKR1C1 0.65 0.006 0.78 0.044 AKT1 0.720.020 AKT3 0.75 <.001 ALDH1A2 0.53 <.001 0.60 <.001 AMPD3 0.62 <.0010.78 0.028 ANPEP 0.54 <.001 0.61 <.001 ANXA2 0.63 0.008 0.74 0.016ARHGAP29 0.67 0.005 0.77 0.016 ARHGDIB 0.64 0.013 ATP5J 0.57 0.050 ATXN10.61 0.004 0.77 0.043 AXIN2 0.51 <.001 0.62 <.001 AZGP1 0.61 <.001 0.64<.001 BCL2 0.64 0.004 0.75 0.029 BIN1 0.52 <.001 0.74 0.010 BTG3 0.750.032 0.75 0.010 BTRC 0.69 0.011 C7 0.51 <.001 0.67 <.001 CADM1 0.49<.001 0.76 0.034 CASP1 0.71 0.010 0.74 0.007 CAV1 0.73 0.015 CCL5 0.670.018 0.67 0.003 CCNH 0.63 <.001 0.75 0.004 CCR1 0.77 0.032 CD164 0.52<.001 0.63 <.001 CD44 0.53 <.001 0.74 0.014 CDH10 0.69 0.040 CDH18 0.400.011 CDK14 0.75 0.013 CDK2 0.81 0.031 CDK3 0.73 0.022 CDKN1A 0.68 0.038CDKN1C 0.62 0.003 0.72 0.005 COL6A1 0.54 <.001 0.70 0.004 COL6A3 0.640.004 CSF1 0.56 <.001 0.78 0.047 CSRP1 0.40 <.001 0.66 0.002 CTGF 0.660.015 0.74 0.027 CTNNB1 0.69 0.043 CTSB 0.60 0.002 0.71 0.011 CTSS 0.670.013 CXCL12 0.56 <.001 0.77 0.026 CYP3A5 0.43 <.001 0.63 <.001 CYR610.43 <.001 0.58 <.001 DAG1 0.72 0.012 DARC 0.66 0.016 DDR2 0.65 0.007DES 0.52 <.001 0.74 0.018 DHRS9 0.54 0.007 DICER1 0.70 0.044 DLC1 0.750.021 DLGAP1 0.55 <.001 0.72 0.005 DNM3 0.61 0.001 DPP4 0.55 <.001 0.770.024 DPT 0.48 <.001 0.61 <.001 DUSP1 0.47 <.001 0.59 <.001 DUSP6 0.650.009 0.65 0.002 DYNLL1 0.74 0.045 EDNRA 0.61 0.002 0.75 0.038 EFNB20.71 0.043 EGR1 0.43 <.001 0.58 <.001 EGR3 0.47 <.001 0.66 <.001 EIF50.77 0.028 ELK4 0.49 <.001 0.72 0.012 EPHA2 0.70 0.007 EPHA3 0.62 <.0010.72 0.009 EPHB2 0.68 0.009 ERBB2 0.64 <.001 0.63 <.001 ERBB3 0.69 0.018ERCC1 0.69 0.019 0.77 0.021 ESR2 0.61 0.020 FAAH 0.57 <.001 0.77 0.035FABP5 0.67 0.035 FAM107A 0.42 <.001 0.59 <.001 FAM13C 0.53 <.001 0.59<.001 FAS 0.71 0.035 FASLG 0.56 0.017 0.67 0.014 FGF10 0.57 0.002 FGF170.70 0.039 0.70 0.010 FGF7 0.63 0.005 0.70 0.004 FGFR2 0.63 0.003 0.710.003 FKBP5 0.72 0.020 FLNA 0.48 <.001 0.74 0.022 FOS 0.45 <.001 0.56<.001 FOXO1 0.59 <.001 FOXQ1 0.57 <.001 0.69 0.008 FYN 0.62 0.001 0.740.013 G6PD 0.77 0.014 GADD45A 0.73 0.045 GADD45B 0.45 <.001 0.64 0.001GDF15 0.58 <.001 GHR 0.62 0.008 0.68 0.002 GPM6B 0.60 <.001 0.70 0.003GSK3B 0.71 0.016 0.71 0.006 GSN 0.46 <.001 0.66 <.001 GSTM1 0.56 <.0010.62 <.001 GSTM2 0.47 <.001 0.67 <.001 HGD 0.72 0.002 HIRIP3 0.69 0.0210.69 0.002 HK1 0.68 0.005 0.73 0.005 HLA-G 0.54 0.024 0.65 0.013 HLF0.41 <.001 0.68 0.001 HNF1B 0.55 <.001 0.59 <.001 HPS1 0.74 0.015 0.760.025 HSD17B3 0.65 0.031 HSPB2 0.62 0.004 0.76 0.027 ICAM1 0.61 0.010IER3 0.55 <.001 0.67 0.003 IFIT1 0.57 <.001 0.70 0.008 IFNG 0.69 0.040IGF1 0.63 <.001 0.59 <.001 IGF2 0.67 0.019 0.70 0.005 IGFBP2 0.53 <.0010.63 <.001 IGFBP5 0.57 <.001 0.71 0.006 IGFBP6 0.41 <.001 0.71 0.012IL10 0.59 0.020 IL1B 0.53 <.001 0.70 0.005 IL6 0.55 0.001 IL6ST 0.45<.001 0.68 <.001 IL8 0.60 0.005 0.70 0.008 ILK 0.68 0.029 0.76 0.036ING5 0.54 <.001 0.82 0.033 ITGA1 0.66 0.017 ITGA3 0.70 0.020 ITGA5 0.640.011 ITGA6 0.66 0.003 0.74 0.006 ITGA7 0.50 <.001 0.71 0.010 ITGB4 0.630.014 0.73 0.010 ITPR1 0.55 <.001 ITPR3 0.76 0.007 JUN 0.37 <.001 0.54<.001 JUNB 0.58 0.002 0.71 0.016 KCTD12 0.68 0.017 KIT 0.49 0.002 0.760.043 KLC1 0.61 0.005 0.77 0.045 KLF6 0.65 0.009 KLK1 0.68 0.036 KLK100.76 0.037 KLK2 0.64 <.001 0.73 0.006 KLK3 0.65 <.001 0.76 0.021 KLRK10.63 0.005 KRT15 0.52 <.001 0.58 <.001 KRT18 0.46 <.001 KRT5 0.51 <.0010.58 <.001 KRT8 0.53 <.001 L1CAM 0.65 0.031 LAG3 0.58 0.002 0.76 0.033LAMA4 0.52 0.018 LAMB3 0.60 0.002 0.65 0.003 LGALS3 0.52 <.001 0.710.002 LIG3 0.65 0.011 LRP1 0.61 0.001 0.75 0.040 MGMT 0.66 0.003 MICA0.59 0.001 0.68 0.001 MLXIP 0.70 0.020 MMP2 0.68 0.022 MMP9 0.67 0.036MPPED2 0.57 <.001 0.66 <.001 MRC1 0.69 0.028 MTSS1 0.63 0.005 0.79 0.037MVP 0.62 <.001 MYBPC1 0.53 <.001 0.70 0.011 NCAM1 0.70 0.039 0.77 0.042NCAPD3 0.52 <.001 0.59 <.001 NDRG1 0.69 0.008 NEXN 0.62 0.002 NFAT5 0.45<.001 0.59 <.001 NFATC2 0.68 0.035 0.75 0.036 NFKBIA 0.70 0.030 NRG10.59 0.022 0.71 0.018 OAZ1 0.69 0.018 0.62 <.001 OLFML3 0.59 <.001 0.720.003 OR51E2 0.73 0.013 PAGE4 0.42 <.001 0.62 <.001 PCA3 0.53 <.001PCDHGB7 0.70 0.032 PGF 0.68 0.027 0.71 0.013 PGR 0.76 0.041 PIK3C2A 0.80<.001 PIK3CA 0.61 <.001 0.80 0.036 PIK3CG 0.67 0.001 0.76 0.018 PLP20.65 0.015 0.72 0.010 PPAP2B 0.45 <.001 0.69 0.003 PPP1R12A 0.61 0.0070.73 0.017 PRIMA1 0.51 <.001 0.68 0.004 PRKCA 0.55 <.001 0.74 0.009PRKCB 0.55 <.001 PROM1 0.67 0.042 PROS1 0.73 0.036 PTCH1 0.69 0.024 0.720.010 PTEN 0.54 <.001 0.64 <.001 PTGS2 0.48 <.001 0.55 <.001 PTH1R 0.570.003 0.77 0.050 PTHLH 0.55 0.010 PTK2B 0.56 <.001 0.70 0.001 PYCARD0.73 0.009 RAB27A 0.65 0.009 0.71 0.014 RAB30 0.59 0.003 0.72 0.010 RAGE0.76 0.011 RARB 0.59 <.001 0.63 <.001 RASSF1 0.67 0.003 RB1 0.67 0.006RFX1 0.71 0.040 0.70 0.003 RHOA 0.71 0.038 0.65 <.001 RHOB 0.58 0.0010.71 0.006 RND3 0.54 <.001 0.69 0.003 RNF114 0.59 0.004 0.68 0.003SCUBE2 0.77 0.046 SDHC 0.72 0.028 0.76 0.025 SEC23A 0.75 0.029 SEMA3A0.61 0.004 0.72 0.011 SEPT9 0.66 0.013 0.76 0.036 SERPINB5 0.75 0.039SH3RF2 0.44 <.001 0.48 <.001 SHH 0.74 0.049 SLC22A3 0.42 <.001 0.61<.001 SMAD4 0.45 <.001 0.66 <.001 SMARCD1 0.69 0.016 SOD1 0.68 0.042SORBS1 0.51 <.001 0.73 0.012 SPARCL1 0.58 <.001 0.77 0.040 SPDEF 0.77<.001 SPINT1 0.65 0.004 0.79 0.038 SRC 0.61 <.001 0.69 0.001 SRD5A2 0.39<.001 0.55 <.001 ST5 0.61 <.001 0.73 0.012 STAT1 0.64 0.006 STAT3 0.630.010 STAT5A 0.62 0.001 0.70 0.003 STAT5B 0.58 <.001 0.73 0.009 SUMO10.66 <.001 SVIL 0.57 0.001 0.74 0.022 TBP 0.65 0.002 TFF1 0.65 0.021TFF3 0.58 <.001 TGFB1I1 0.51 <.001 0.75 0.026 TGFB2 0.48 <.001 0.62<.001 TGFBR2 0.61 0.003 TIAM1 0.68 0.019 TIMP2 0.69 0.020 TIMP3 0.580.002 TNFRSF10A 0.73 0.047 TNFRSF10B 0.47 <.001 0.70 0.003 TNFSF10 0.560.001 TP63 0.67 0.001 TPM1 0.58 0.004 0.73 0.017 TPM2 0.46 <.001 0.700.005 TRA2A 0.68 0.013 TRAF3IP2 0.73 0.041 0.71 0.004 TRO 0.72 0.0160.71 0.004 TUBB2A 0.53 <.001 0.73 0.021 TYMP 0.70 0.011 VCAM1 0.69 0.041VCL 0.46 <.001 VEGFA 0.77 0.039 VEGFB 0.71 0.035 VIM 0.60 0.001 XRCC50.75 0.026 YY1 0.62 0.008 0.77 0.039 ZFHX3 0.53 <.001 0.58 <.001 ZFP360.43 <.001 0.54 <.001 ZNF827 0.55 0.001

Tables 8A and 8B provide genes that were significantly associated(p<0.05), positively or negatively, with clinical recurrence (cRFI) inpositive TMPRSS fusion specimens in the primary or highest Gleasonpattern specimen. Increased expression of genes in Table 8A isnegatively associated with good prognosis, while increased expression ofgenes in Table 8B is positively associated with good prognosis.

TABLE 8A Genes significantly (p < 0.05) associated with cRFI forTMPRSS2-ERG fusion positive in the primary Gleason pattern or highestGleason pattern with hazard ratio (HR) >1.0 (increased expression isnegatively associated with good prognosis) Official Primary PatternHighest Pattern Symbol HR p-value HR p-value ACTR2 1.78 0.017 AKR1C31.44 0.013 ALCAM 1.44 0.022 ANLN 1.37 0.046 1.81 <.001 APOE 1.49 0.0231.66 0.005 AQP2 1.30 0.013 ARHGDIB 1.55 0.021 ASPN 2.13 <.001 2.43 <.001ATP5E 1.69 0.013 1.58 0.014 BGN 1.92 <.001 2.55 <.001 BIRC5 1.48 0.0061.89 <.001 BMP6 1.51 0.010 1.96 <.001 BRCA2 1.41 0.007 BUB1 1.36 0.0071.52 <.001 CCNE2 1.55 0.004 1.59 <.001 CD276 1.65 <.001 CDC20 1.68 <.0011.74 <.001 CDH11 1.50 0.017 CDH18 1.36 <.001 CDH7 1.54 0.009 1.46 0.026CDKN2B 1.68 0.008 1.93 0.001 CDKN2C 2.01 <.001 1.77 <.001 CDKN3 1.510.002 1.33 0.049 CENPF 1.51 0.007 2.04 <.001 CKS2 1.43 0.034 1.56 0.007COL1A1 2.23 <.001 3.04 <.001 COL1A2 1.79 0.001 2.22 <.001 COL3A1 1.96<.001 2.81 <.001 COL4A1 1.52 0.020 COL5A1 1.50 0.020 COL5A2 1.64 0.0171.55 0.010 COL8A1 1.96 <.001 2.38 <.001 CRISP3 1.68 0.002 1.67 0.002CTHRC1 2.06 <.001 CTNND2 1.42 0.046 1.50 0.025 CTSK 1.43 0.049 CXCR41.82 0.001 1.64 0.007 DDIT4 1.54 0.016 1.58 0.009 DLL4 1.51 0.007 DYNLL11.50 0.021 1.22 0.002 F2R 2.27 <.001 2.02 <.001 FAP 2.12 <.001 FCGR3A1.94 0.002 FGF5 1.23 0.047 FOXP3 1.52 0.006 1.48 0.018 GNPTAB 1.44 0.042GPR68 1.51 0.011 GREM1 1.91 <.001 2.38 <.001 HDAC1 1.43 0.048 HDAC9 1.65<.001 1.67 0.004 HRAS 1.65 0.005 1.58 0.021 IGFBP3 1.94 <.001 1.85 <.001INHBA 2.03 <.001 2.64 <.001 JAG1 1.41 0.027 1.50 0.008 KCTD12 1.51 0.017KHDRBS3 1.48 0.029 1.54 0.014 KPNA2 1.46 0.050 LAMA3 1.35 0.040 LAMC11.77 0.012 LTBP2 1.82 <.001 LUM 1.51 0.021 1.53 0.009 MELK 1.38 0.0201.49 0.001 MKI67 1.37 0.014 MMP11 1.73 <.001 1.69 <.001 MRPL13 1.300.046 MYBL2 1.56 <.001 1.72 <.001 MYLK3 1.17 0.007 NOX4 1.58 0.005 1.96<.001 NRIP3 1.30 0.040 NRP1 1.53 0.021 OLFML2B 1.54 0.024 OSM 1.43 0.018PATE1 1.20 <.001 1.33 <.001 PCNA 1.64 0.003 PEX10 1.41 0.041 1.64 0.003PIK3CA 1.38 0.037 PLK1 1.52 0.009 1.67 0.002 PLOD2 1.65 0.002 POSTN 1.79<.001 2.06 <.001 PTK6 1.67 0.002 2.38 <.001 PTTG1 1.56 0.002 1.54 0.003RAD21 1.61 0.036 1.53 0.005 RAD51 1.33 0.009 RALA 1.95 0.004 1.60 0.007REG4 1.43 0.042 ROBO2 1.46 0.024 RRM1 1.44 0.033 RRM2 1.50 0.003 1.48<.001 SAT1 1.42 0.009 1.43 0.012 SEC14L1 1.64 0.002 SFRP4 2.07 <.0012.40 <.001 SHMT2 1.52 0.030 1.60 0.001 SLC44A1 1.42 0.039 SPARC 1.93<.001 2.21 <.001 SULF1 1.63 0.006 2.04 <.001 THBS2 1.95 <.001 2.26 <.001THY1 1.69 0.016 1.95 0.002 TK1 1.43 0.003 TOP2A 1.57 0.002 2.11 <.001TPX2 1.84 <.001 2.27 <.001 UBE2C 1.41 0.011 1.44 0.006 UBE2T 1.63 0.001UHRF1 1.51 0.007 1.69 <.001 WISP1 1.47 0.045 WNT5A 1.35 0.027 1.63 0.001ZWINT 1.36 0.045

TABLE 8B Genes significantly (p < 0.05) associated with cRFI forTMPRSS2-ERG fusion positive in the primary Gleason pattern or highestGleason pattern with hazard ratio (HR) <1.0 (increased expression ispositively associated with good prognosis) Official Primary PatternHighest Pattern Symbol HR p-value HR p-value AAMP 0.57 0.007 0.58 <.001ABCA5 0.80 0.044 ACE 0.65 0.023 0.55 <.001 ACOX2 0.55 <.001 ADH5 0.680.022 AKAP1 0.81 0.043 ALDH1A2 0.72 0.036 0.43 <.001 ANPEP 0.66 0.0220.46 <.001 APRT 0.73 0.040 AXIN2 0.60 <.001 AZGP1 0.57 <.001 0.65 <.001BCL2 0.69 0.035 BIK 0.71 0.045 BIN1 0.71 0.004 0.71 0.009 BTRC 0.660.003 0.58 <.001 C7 0.64 0.006 CADM1 0.61 <.001 0.47 <.001 CCL2 0.730.042 CCNH 0.69 0.022 CD44 0.56 <.001 0.58 <.001 CD82 0.72 0.033 CDC25B0.74 0.028 CDH1 0.75 0.030 0.72 0.010 CDH19 0.56 0.015 CDK3 0.78 0.045CDKN1C 0.74 0.045 0.70 0.014 CSF1 0.72 0.037 CTSB 0.69 0.048 CTSL2 0.580.005 CYP3A5 0.51 <.001 0.30 <.001 DHX9 0.89 0.006 0.87 0.012 DLC1 0.640.023 DLGAP1 0.69 0.010 0.49 <.001 DPP4 0.64 <.001 0.56 <.001 DPT 0.630.003 EGR1 0.69 0.035 EGR3 0.68 0.025 EIF2S3 0.70 0.021 EIF5 0.71 0.030ELK4 0.71 0.041 0.60 0.003 EPHA2 0.72 0.036 0.66 0.011 EPHB4 0.65 0.007ERCC1 0.68 0.023 ESR2 0.64 0.027 FAM107A 0.64 0.003 0.61 0.003 FAM13C0.68 0.006 0.55 <.001 FGFR2 0.73 0.033 0.59 <.001 FKBP5 0.60 0.006 FLNC0.68 0.024 0.65 0.012 FLT1 0.71 0.027 FOS 0.62 0.006 FOXO1 0.75 0.010GADD45B 0.68 0.020 GHR 0.62 0.006 GPM6B 0.57 <.001 GSTM1 0.68 0.015 0.58<.001 GSTM2 0.65 0.005 0.47 <.001 HGD 0.63 0.001 0.71 0.020 HK1 0.670.003 0.62 0.002 HLF 0.59 <.001 HNF1B 0.66 0.004 0.61 0.001 IER3 0.700.026 IGF1 0.63 0.005 0.55 <.001 IGF1R 0.76 0.049 IGFBP2 0.59 0.007 0.640.003 IL6ST 0.65 0.005 IL8 0.61 0.005 0.66 0.019 ILK 0.64 0.015 ING50.73 0.033 0.70 0.009 ITGA7 0.72 0.045 0.69 0.019 ITGB4 0.63 0.002 KLC10.74 0.045 KLK1 0.56 0.002 0.49 <.001 KLK10 0.68 0.013 KLK11 0.66 0.003KLK2 0.66 0.045 0.65 0.011 KLK3 0.75 0.048 0.77 0.014 KRT15 0.71 0.0170.50 <.001 KRT5 0.73 0.031 0.54 <.001 LAMA5 0.70 0.044 LAMB3 0.70 0.0050.58 <.001 LGALS3 0.69 0.025 LIG3 0.68 0.022 MDK 0.69 0.035 MGMT 0.590.017 0.60 <.001 MGST1 0.73 0.042 MICA 0.70 0.009 MPPED2 0.72 0.031 0.54<.001 MTSS1 0.62 0.003 MYBPC1 0.50 <.001 NCAPD3 0.62 0.007 0.38 <.001NCOR1 0.82 0.048 NFAT5 0.60 0.001 0.62 <.001 NRG1 0.66 0.040 0.61 0.029NUP62 0.75 0.037 OMD 0.54 <.001 PAGE4 0.64 0.005 PCA3 0.66 0.012 PCDHGB70.68 0.018 PGR 0.60 0.012 PPAP2B 0.62 0.010 PPP1R12A 0.73 0.031 0.580.003 PRIMA1 0.65 0.013 PROM1 0.41 0.013 PTCH1 0.64 0.006 PTEN 0.750.047 PTGS2 0.67 0.011 PTK2B 0.66 0.005 PTPN1 0.71 0.026 RAGE 0.70 0.012RARB 0.68 0.016 RGS10 0.84 0.034 RHOB 0.66 0.016 RND3 0.63 0.004 SDHC0.73 0.044 0.69 0.016 SERPINA3 0.67 0.011 0.51 <.001 SERPINB5 0.42 <.001SH3RF2 0.66 0.012 0.51 <.001 SLC22A3 0.59 0.003 0.48 <.001 SMAD4 0.640.004 0.49 <.001 SMARCC2 0.73 0.042 SMARCD1 0.73 <.001 0.76 0.035 SMO0.64 0.006 SNAI1 0.53 0.008 SOD1 0.60 0.003 SRC 0.64 <.001 0.61 <.001SRD5A2 0.63 0.004 0.59 <.001 STAT3 0.64 0.014 STAT5A 0.70 0.032 STAT5B0.74 0.034 0.63 0.003 SVIL 0.71 0.028 TGFB1I1 0.68 0.036 TMPRSS2 0.720.015 0.67 <.001 TNFRSF10A 0.69 0.010 TNFRSF10B 0.67 0.007 0.64 0.001TNFRSF18 0.38 0.003 TNFSF10 0.71 0.025 TP53 0.68 0.004 0.57 <.001 TP630.75 0.049 0.52 <.001 TPM2 0.62 0.007 TRAF3IP2 0.71 0.017 0.68 0.005 TRO0.72 0.033 TUBB2A 0.69 0.038 VCL 0.62 <.001 VEGFA 0.71 0.037 WWOX 0.650.004 ZFHX3 0.77 0.011 0.73 0.012 ZFP36 0.69 0.018 ZNF827 0.68 0.0130.49 <.001

Tables 9A and 9B provide genes significantly associated (p<0.05),positively or negatively, with TMPRSS fusion status in the primaryGleason pattern. Increased expression of genes in Table 9A arepositively associated with TMPRSS fusion positivity, while increasedexpression of genes in Table 10A are negatively associated with TMPRSSfusion positivity.

TABLE 9A Genes significantly (p < 0.05) associated with TMPRSS fusionstatus in the primary Gleason pattern with odds ratio (OR) >1.0(increased expression is positively associated with TMPRSS fusionpositivity Official Symbol p-value Odds Ratio ABCC8 <.001 1.86 ALDH18A10.005 1.49 ALKBH3 0.043 1.30 ALOX5 <.001 1.66 AMPD3 <.001 3.92 APEX1<.001 2.00 ARHGDIB <.001 1.87 ASAP2 0.019 1.48 ATXN1 0.013 1.41 BMPR1B<.001 2.37 CACNA1D <.001 9.01 CADPS 0.015 1.39 CD276 0.003 2.25 CDH10.016 1.37 CDH7 <.001 2.22 CDK7 0.025 1.43 COL9A2 <.001 2.58 CRISP3<.001 2.60 CTNND1 0.033 1.48 ECE1 <.001 2.22 EIF5 0.023 1.34 EPHB4 0.0051.51 ERG <.001 14.5  FAM171B 0.047 1.32 FAM73A 0.008 1.45 FASN 0.0041.50 GNPTAB <.001 1.60 GPS1 0.006 1.45 GRB7 0.023 1.38 HDAC1 <.001 4.95HGD <.001 1.64 HIP1 <.001 1.90 HNF1B <.001 3.55 HSPA8 0.041 1.32 IGF1R0.001 1.73 ILF3 <.001 1.91 IMMT 0.025 1.36 ITPR1 <.001 2.72 ITPR3 <.0015.91 JAG1 0.007 1.42 KCNN2 <.001 2.80 KHDRBS3 <.001 2.63 KIAA0247 0.0191.38 KLK11 <.001 1.98 LAMC1 0.008 1.56 LAMC2 <.001 3.30 LOX 0.009 1.41LRP1 0.044 1.30 MAP3K5 <.001 2.06 MAP7 <.001 2.74 MSH2 0.005 1.59 MSH30.006 1.45 MUC1 0.012 1.42 MYO6 <.001 3.79 NCOR2 0.001 1.62 NDRG1 <.0016.77 NETO2 <.001 2.63 ODC1 <.001 1.98 OR51E1 <.001 2.24 PDE9A <.001 2.21PEX10 <.001 3.41 PGK1 0.022 1.33 PLA2G7 <.001 5.51 PPP3CA 0.047 1.38PSCA 0.013 1.43 PSMD13 0.004 1.51 PTCH1 0.022 1.38 PTK2 0.014 1.38 PTK6<.001 2.29 PTK7 <.001 2.45 PTPRK <.001 1.80 RAB30 0.001 1.60 REG4 0.0181.58 RELA 0.001 1.62 RFX1 0.020 1.43 RGS10 <.001 1.71 SCUBE2 0.009 1.48SEPT9 <.001 3.91 SH3RF2 0.004 1.48 SH3YL1 <.001 1.87 SHH <.001 2.45 SIM2<.001 1.74 SIPA1L1 0.021 1.35 SLC22A3 <.001 1.63 SLC44A1 <.001 1.65SPINT1 0.017 1.39 TFDP1 0.005 1.75 TMPRSS2ERGA 0.002 14E5 TMPRSS2ERGB<.001 1.97 TRIM14 <.001 1.65 TSTA3 0.018 1.38 UAP1 0.046 1.39 UBE2G10.001 1.66 UGDH <.001 2.22 XRCC5 <.001 1.66 ZMYND8 <.001 2.19

TABLE 9B Genes significantly (p < 0.05) associated with TMPRSS fusionstatus in the primary Gleason pattern with odds ratio (OR) <1.0(increased expression is negatively associated with TMPRSS fusionpositivity) Official Symbol p-value Odds Ratio ABCC4 0.045 0.77 ABHD2<.001 0.38 ACTR2 0.027 0.73 ADAMTS1 0.024 0.58 ADH5 <.001 0.58 AGTR20.016 0.64 AKAP1 0.013 0.70 AKT2 0.015 0.71 ALCAM <.001 0.45 ALDH1A20.004 0.70 ANPEP <.001 0.43 ANXA2 0.010 0.71 APC 0.036 0.73 APOC1 0.0020.56 APOE <.001 0.44 ARF1 0.041 0.77 ATM 0.036 0.74 AURKB <.001 0.62AZGP1 <.001 0.54 BBC3 0.030 0.74 BCL2 0.012 0.70 BIN1 0.021 0.74 BTG10.004 0.67 BTG3 0.003 0.63 C7 0.023 0.74 CADM1 0.007 0.69 CASP1 0.0110.70 CAV1 0.011 0.71 CCND1 0.019 0.72 CCR1 0.022 0.73 CD44 <.001 0.57CD68 <.001 0.54 CD82 0.002 0.66 CDH5 0.007 0.66 CDKN1A <.001 0.60 CDKN2B<.001 0.54 CDKN2C 0.012 0.72 CDKN3 0.037 0.77 CHN1 0.038 0.75 CKS2 <.0010.48 COL11A1 0.017 0.72 COL1A1 <.001 0.59 COL1A2 0.001 0.62 COL3A1 0.0270.73 COL4A1 0.043 0.76 COL5A1 0.039 0.74 COL5A2 0.026 0.73 COL6A1 0.0080.66 COL6A3 <.001 0.59 COL8A1 0.022 0.74 CSF1 0.011 0.70 CTNNB1 0.0210.69 CTSB <.001 0.62 CTSD 0.036 0.68 CTSK 0.007 0.70 CTSS 0.002 0.64CXCL12 <.001 0.48 CXCR4 0.005 0.68 CXCR7 0.046 0.76 CYR61 0.004 0.65 DAP0.002 0.64 DARC 0.021 0.73 DDR2 0.021 0.73 DHRS9 <.001 0.52 DIAPH1 <.0010.56 DICER1 0.029 0.75 DLC1 0.013 0.72 DLGAP1 <.001 0.60 DLL4 <.001 0.57DPT 0.006 0.68 DUSP1 0.012 0.68 DUSP6 0.001 0.62 DVL1 0.037 0.75 EFNB2<.001 0.32 EGR1 0.003 0.65 ELK4 <.001 0.60 ERBB2 <.001 0.61 ERBB3 0.0450.76 ESR2 0.010 0.70 ETV1 0.042 0.74 FABP5 <.001 0.21 FAM13C 0.006 0.67FCGR3A 0.018 0.72 FGF17 0.009 0.71 FGF6 0.011 0.70 FGF7 0.003 0.63 FN10.006 0.69 FOS 0.035 0.74 FOXP3 0.010 0.71 GABRG2 0.029 0.74 GADD45B0.003 0.63 GDF15 <.001 0.54 GPM6B 0.004 0.67 GPNMB 0.001 0.62 GSN 0.0090.69 HLA-G 0.050 0.74 HLF 0.018 0.74 HPS1 <.001 0.48 HSD17B3 0.003 0.60HSD17B4 <.001 0.56 HSPB1 <.001 0.38 HSPB2 0.002 0.62 IFI30 0.049 0.75IFNG 0.006 0.64 IGF1 0.016 0.73 IGF2 0.001 0.57 IGFBP2 <.001 0.51 IGFBP3<.001 0.59 IGFBP6 <.001 0.57 IL10 <.001 0.62 IL17A 0.012 0.63 IL1A 0.0110.59 IL2 0.001 0.63 IL6ST <.001 0.52 INSL4 0.014 0.71 ITGA1 0.009 0.69ITGA4 0.007 0.68 JUN <.001 0.59 KIT <.001 0.64 KRT76 0.016 0.70 LAG30.002 0.63 LAPTM5 <.001 0.58 LGALS3 <.001 0.53 LTBP2 0.011 0.71 LUM0.012 0.70 MAOA 0.020 0.73 MAP4K4 0.007 0.68 MGST1 <.001 0.54 MMP2 <.0010.61 MPPED2 <.001 0.45 MRC1 0.005 0.67 MTPN 0.002 0.56 MTSS1 <.001 0.53MVP 0.009 0.72 MYBPC1 <.001 0.51 MYLK3 0.001 0.58 NCAM1 <.001 0.59NCAPD3 <.001 0.40 NCOR1 0.004 0.69 NFKBIA <.001 0.63 NNMT 0.006 0.66NPBWR1 0.027 0.67 OAZ1 0.049 0.64 OLFML3 <.001 0.56 OSM <.001 0.64 PAGE10.012 0.52 PDGFRB 0.016 0.73 PECAM1 <.001 0.55 PGR 0.048 0.77 PIK3CA<.001 0.55 PIK3CG 0.008 0.71 PLAU 0.044 0.76 PLK1 0.006 0.68 PLOD2 0.0130.71 PLP2 0.024 0.73 PNLIPRP2 0.009 0.70 PPAP2B <.001 0.62 PRKAR2B <.0010.61 PRKCB 0.044 0.76 PROS1 0.005 0.67 PTEN <.001 0.47 PTGER3 0.007 0.69PTH1R 0.011 0.70 PTK2B <.001 0.61 PTPN1 0.028 0.73 RAB27A <.001 0.21RAD51 <.001 0.51 RAD9A 0.030 0.75 RARB <.001 0.62 RASSF1 0.038 0.76 RECK0.009 0.62 RHOB 0.004 0.64 RHOC <.001 0.56 RLN1 <.001 0.30 RND3 0.0140.72 S100P 0.002 0.66 SDC2 <.001 0.61 SEMA3A 0.001 0.64 SMAD4 <.001 0.64SPARC <.001 0.59 SPARCL1 <.001 0.56 SPINK1 <.001 0.26 SRD5A1 0.039 0.76STAT1 0.026 0.74 STS 0.006 0.64 SULF1 <.001 0.53 TFF3 <.001 0.19 TGFA0.002 0.65 TGFB1I1 0.040 0.77 TGFB2 0.003 0.66 TGFB3 <.001 0.54 TGFBR2<.001 0.61 THY1 <.001 0.63 TIMP2 0.004 0.66 TIMP3 <.001 0.60 TMPRSS2<.001 0.40 TNFSF11 0.026 0.63 TPD52 0.002 0.64 TRAM1 <.001 0.45 TRPC60.002 0.64 TUBB2A <.001 0.49 VCL <.001 0.57 VEGFB 0.033 0.73 VEGFC <.0010.61 VIM 0.012 0.69 WISP1 0.030 0.75 WNT5A <.001 0.50

A molecular field effect was investigated, and determined that theexpression levels of histologically normal-appearing cells adjacent tothe tumor exhibited a molecular signature of prostate cancer. Tables 10Aand 10B provide genes significantly associated (p<0.05), positively ornegatively, with cRFI or bRFI in non-tumor samples. Table 10A isnegatively associated with good prognosis, while increased expression ofgenes in Table 10B is positively associated with good prognosis.

TABLE 10A Genes significantly (p < 0.05) associated with cRFI or bRFI inNon-Tumor Samples with hazard ratio (HR) >1.0 (increased expression isnegatively associated with good prognosis) Official cRFI bRFI Symbol HRp-value HR p-value ALCAM 1.278 0.036 ASPN 1.309 0.032 BAG5 1.458 0.004BRCA2 1.385 <.001 CACNA1D 1.329 0.035 CD164 1.339 0.020 CDKN2B 1.3980.014 COL3A1 1.300 0.035 COL4A1 1.358 0.019 CTNND2 1.370 0.001 DARC1.451 0.003 DICER1 1.345 <.001 DPP4 1.358 0.008 EFNB2 1.323 0.007 FASN1.327 0.035 GHR 1.332 0.048 HSPA5 1.260 0.048 INHBA 1.558 <.001 KCNN21.264 0.045 KRT76 1.115 <.001 LAMC1 1.390 0.014 LAMC2 1.216 0.042 LIG31.313 0.030 MAOA 1.405 0.013 MCM6 1.307 0.036 MKI67 1.271 0.008 NEK21.312 0.016 NPBWR1 1.278 0.035 ODC1 1.320 0.010 PEX10 1.361 0.014 PGK11.488 0.004 PLA2G7 1.337 0.025 POSTN 1.306 0.043 PTK6 1.344 0.005 REG41.348 0.009 RGS7 1.144 0.047 SFRP4 1.394 0.009 TARP 1.412 0.011 TFF11.346 0.010 TGFBR2 1.310 0.035 THY1 1.300 0.038 TMPRSS2ERGA 1.333 <.001TPD52 1.374 0.015 TRPC6 1.272 0.046 UBE2C 1.323 0.007 UHRF1 1.325 0.021

TABLE 10B Genes significantly (p < 0.05) associated with cRFI or bRFI inNon-Tumor Samples with hazard ratio (HR) <1.0 (increased expression ispositively associated with good prognosis) Official cRFI bRFI Symbol HRp-value HR p-value ABCA5 0.807 0.028 ABCC3 0.760 0.019 0.750 0.003 ABHD20.781 0.028 ADAM15 0.718 0.005 AKAP1 0.740 0.009 AMPD3 0.793 0.013ANGPT2 0.752 0.027 ANXA2 0.776 0.035 APC 0.755 0.014 APRT 0.762 0.025 AR0.752 0.015 ARHGDIB 0.753 <.001 BIN1 0.738 0.016 CADM1 0.711 0.004 CCNH0.820 0.041 CCR1 0.749 0.007 CDK14 0.772 0.014 CDK3 0.819 0.044 CDKN1C0.808 0.038 CHAF1A 0.634 0.002 0.779 0.045 CHN1 0.803 0.034 CHRAC1 0.7510.014 0.779 0.021 COL5A1 0.736 0.012 COL5A2 0.762 0.013 COL6A1 0.7570.032 COL6A3 0.757 0.019 CSK 0.663 <.001 0.698 <.001 CTSK 0.782 0.029CXCL12 0.771 0.037 CXCR7 0.753 0.008 CYP3A5 0.790 0.035 DDIT4 0.7250.017 DIAPH1 0.771 0.015 DLC1 0.744 0.004 0.807 0.015 DLGAP1 0.708 0.004DUSP1 0.740 0.034 EDN1 0.742 0.010 EGR1 0.731 0.028 EIF3H 0.761 0.024EIF4E 0.786 0.041 ERBB2 0.664 0.001 ERBB4 0.764 0.036 ERCC1 0.804 0.041ESR2 0.757 0.025 EZH2 0.798 0.048 FAAH 0.798 0.042 FAM13C 0.764 0.012FAM171B 0.755 0.005 FAM49B 0.811 0.043 FAM73A 0.778 0.015 FASLG 0.7570.041 FGFR2 0.735 0.016 FOS 0.690 0.008 FYN 0.788 0.035 0.777 0.011GPNMB 0.762 0.011 GSK3B 0.792 0.038 HGD 0.774 0.017 HIRIP3 0.802 0.033HSP90AB1 0.753 0.013 HSPB1 0.764 0.021 HSPE1 0.668 0.001 IFI30 0.7320.002 IGF2 0.747 0.006 IGFBP5 0.691 0.006 IL6ST 0.748 0.010 IL8 0.7850.028 IMMT 0.708 <.001 ITGA6 0.747 0.008 ITGAV 0.792 0.016 ITGB3 0.8140.034 ITPR3 0.769 0.009 JUN 0.655 0.005 KHDRBS3 0.764 0.012 KLF6 0.714<.001 KLK2 0.813 0.048 LAMA4 0.702 0.009 LAMA5 0.744 0.011 LAPTM5 0.7400.009 LGALS3 0.773 0.036 0.788 0.024 LIMS1 0.807 0.012 MAP3K5 0.8150.034 MAP3K7 0.809 0.032 MAP4K4 0.735 0.018 0.761 0.010 MAPKAPK3 0.7540.014 MICA 0.785 0.019 MTA1 0.808 0.043 MVP 0.691 0.001 MYLK3 0.7300.039 MYO6 0.780 0.037 NCOA1 0.787 0.040 NCOR1 0.876 0.020 NDRG1 0.761<.001 NFAT5 0.770 0.032 NFKBIA 0.799 0.018 NME2 0.753 0.005 NUP62 0.8420.032 OAZ1 0.803 0.043 OLFML2B 0.745 0.023 OLFML3 0.743 0.009 OSM 0.7260.018 PCA3 0.714 0.019 PECAM1 0.774 0.023 PIK3C2A 0.768 0.001 PIM1 0.7250.011 PLOD2 0.713 0.008 PPP3CA 0.768 0.040 PROM1 0.482 <.001 PTEN 0.8070.012 PTGS2 0.726 0.011 PTTG1 0.729 0.006 PYCARD 0.783 0.012 RAB30 0.7300.002 RAGE 0.792 0.012 RFX1 0.789 0.016 0.792 0.010 RGS10 0.781 0.017RUNX1 0.747 0.007 SDHC 0.827 0.036 SEC23A 0.752 0.010 SEPT9 0.889 0.006SERPINA3 0.738 0.013 SLC25A21 0.788 0.045 SMARCD1 0.788 0.010 0.7330.007 SMO 0.813 0.035 SRC 0.758 0.026 SRD5A2 0.738 0.005 ST5 0.767 0.022STAT5A 0.784 0.039 TGFB2 0.771 0.027 TGFB3 0.752 0.036 THBS2 0.751 0.015TNFRSF10B 0.739 0.010 TPX2 0.754 0.023 TRAF3IP2 0.774 0.015 TRAM1 0.868<.001 0.880 <.001 TRIM14 0.785 0.047 TUBB2A 0.705 0.010 TYMP 0.778 0.024UAP1 0.721 0.013 UTP23 0.763 0.007 0.826 0.018 VCL 0.837 0.040 VEGFA0.755 0.009 WDR19 0.724 0.005 YBX1 0.786 0.027 ZFP36 0.744 0.032 ZNF8270.770 0.043

Table 11 provides genes that are significantly associated (p<0.05) withcRFI or bRFI after adjustment for Gleason pattern or highest Gleasonpattern.

TABLE 11 Genes significantly (p < 0.05) associated with cRFI or bRFIafter adjustment for Gleason pattern in the primary Gleason pattern orhighest Gleason pattern Some HR <=1.0 and some HR >1.0 cRFI bRFI bRFIOfficial Highest Pattern Primary Pattern Highest Pattern Symbol HRp-value HR p-value HR p-value HSPA5 0.710 0.009 1.288 0.030 ODC1 0.7410.026 1.343 0.004 1.261 0.046

Tables 12A and 12B provide genes that are significantly associated(p<0.05) with prostate cancer specific survival (PCSS) in the primaryGleason pattern. Increased expression of genes in Table 12A isnegatively associated with good prognosis, while increased expression ofgenes in Table 12B is positively associated with good prognosis.

TABLE 12A Genes significantly (p < 0.05) associated with prostate cancerspecific survival (PCSS) in the Primary Gleason Pattern HR >1.0(Increased expression is negatively associated with good prognosis)Official Symbol HR p-value AKR1C3 1.476 0.016 ANLN 1.517 0.006 APOC11.285 0.016 APOE 1.490 0.024 ASPN 3.055 <.001 ATP5E 1.788 0.012 AURKB1.439 0.008 BGN 2.640 <.001 BIRC5 1.611 <.001 BMP6 1.490 0.021 BRCA11.418 0.036 CCNB1 1.497 0.021 CD276 1.668 0.005 CDC20 1.730 <.001 CDH111.565 0.017 CDH7 1.553 0.007 CDKN2B 1.751 0.003 CDKN2C 1.993 0.013 CDKN31.404 0.008 CENPF 2.031 <.001 CHAF1A 1.376 0.011 CKS2 1.499 0.031 COL1A12.574 <.001 COL1A2 1.607 0.011 COL3A1 2.382 <.001 COL4A1 1.970 <.001COL5A2 1.938 0.002 COL8A1 2.245 <.001 CTHRC1 2.085 <.001 CXCR4 1.7830.007 DDIT4 1.535 0.030 DYNLL1 1.719 0.001 F2R 2.169 <.001 FAM171B 1.4300.044 FAP 1.993 0.002 FCGR3A 2.099 <.001 FN1 1.537 0.024 GPR68 1.5200.018 GREM1 1.942 <.001 IFI30 1.482 0.048 IGFBP3 1.513 0.027 INHBA 3.060<.001 KIF4A 1.355 0.001 KLK14 1.187 0.004 LAPTM5 1.613 0.006 LTBP2 2.018<.001 MMP11 1.869 <.001 MYBL2 1.737 0.013 NEK2 1.445 0.028 NOX4 2.049<.001 OLFML2B 1.497 0.023 PLK1 1.603 0.006 POSTN 2.585 <.001 PPFIA31.502 0.012 PTK6 1.527 0.009 PTTG1 1.382 0.029 RAD51 1.304 0.031 RGS71.251 <.001 RRM2 1.515 <.001 SAT1 1.607 0.004 SDC1 1.710 0.007 SESN31.399 0.045 SFRP4 2.384 <.001 SHMT2 1.949 0.003 SPARC 2.249 <.001 STMN11.748 0.021 SULF1 1.803 0.004 THBS2 2.576 <.001 THY1 1.908 0.001 TK11.394 0.004 TOP2A 2.119 <.001 TPX2 2.074 0.042 UBE2C 1.598 <.001 UGT2B151.363 0.016 UHRF1 1.642 0.001 ZWINT 1.570 0.010

TABLE 12B Genes significantly (p < 0.05) associated with prostate cancerspecific survival (PCSS) in the Primary Gleason Pattern HR <1.0(Increased expression is positively associated with good prognosis)Official Symbol HR p-value AAMP 0.649 0.040 ABCA5 0.777 0.015 ABCG20.715 0.037 ACOX2 0.673 0.016 ADH5 0.522 <.001 ALDH1A2 0.561 <.001 AMACR0.693 0.029 AMPD3 0.750 0.049 ANPEP 0.531 <.001 ATXN1 0.640 0.011 AXIN20.657 0.002 AZGP1 0.617 <.001 BDKRB1 0.553 0.032 BIN1 0.658 <.001 BTRC0.716 0.011 C7 0.531 <.001 CADM1 0.646 0.015 CASP7 0.538 0.029 CCNH0.674 0.001 CD164 0.606 <.001 CD44 0.687 0.016 CDK3 0.733 0.039 CHN10.653 0.014 COL6A1 0.681 0.015 CSF1 0.675 0.019 CSRP1 0.711 0.007 CXCL120.650 0.015 CYP3A5 0.507 <.001 CYR61 0.569 0.007 DLGAP1 0.654 0.004 DNM30.692 0.010 DPP4 0.544 <.001 DPT 0.543 <.001 DUSP1 0.660 0.050 DUSP60.699 0.033 EGR1 0.490 <.001 EGR3 0.561 <.001 EIF5 0.720 0.035 ERBB30.739 0.042 FAAH 0.636 0.010 FAM107A 0.541 <.001 FAM13C 0.526 <.001 FAS0.689 0.030 FGF10 0.657 0.024 FKBP5 0.699 0.040 FLNC 0.742 0.036 FOS0.556 0.005 FOXQ1 0.666 0.007 GADD45B 0.554 0.002 GDF15 0.659 0.009 GHR0.683 0.027 GPM6B 0.666 0.005 GSN 0.646 0.006 GSTM1 0.672 0.006 GSTM20.514 <.001 HGD 0.771 0.039 HIRIP3 0.730 0.013 HK1 0.778 0.048 HLF 0.581<.001 HNF1B 0.643 0.013 HSD17B10 0.742 0.029 IER3 0.717 0.049 IGF1 0.612<.001 IGFBP6 0.578 0.003 IL2 0.528 0.010 IL6ST 0.574 <.001 IL8 0.5400.001 ING5 0.688 0.015 ITGA6 0.710 0.005 ITGA7 0.676 0.033 JUN 0.5060.001 KIT 0.628 0.047 KLK1 0.523 0.002 KLK2 0.581 <.001 KLK3 0.676 <.001KRT15 0.684 0.005 KRT18 0.536 <.001 KRT5 0.673 0.004 KRT8 0.613 0.006LAMB3 0.740 0.027 LGALS3 0.678 0.007 MGST1 0.640 0.002 MPPED2 0.629<.001 MTSS1 0.705 0.041 MYBPC1 0.534 <.001 NCAPD3 0.519 <.001 NFAT50.536 <.001 NRG1 0.467 0.007 OLFML3 0.646 0.001 OMD 0.630 0.006 OR51E20.762 0.017 PAGE4 0.518 <.001 PCA3 0.581 <.001 PGF 0.705 0.038 PPAP2B0.568 <.001 PPP1R12A 0.694 0.017 PRIMA1 0.678 0.014 PRKCA 0.632 0.001PRKCB 0.692 0.028 PROM1 0.393 0.017 PTEN 0.689 0.002 PTGS2 0.611 0.004PTH1R 0.629 0.031 RAB27A 0.721 0.046 RND3 0.678 0.029 RNF114 0.714 0.035SDHC 0.590 <.001 SERPINA3 0.710 0.050 SH3RF2 0.570 0.005 SLC22A3 0.517<.001 SMAD4 0.528 <.001 SMO 0.751 0.026 SRC 0.667 0.004 SRD5A2 0.488<.001 STAT5B 0.700 0.040 SVIL 0.694 0.024 TFF3 0.701 0.045 TGFB1I1 0.6700.029 TGFB2 0.646 0.010 TNFRSF10B 0.685 0.014 TNFSF10 0.532 <.001 TPM20.623 0.005 TRO 0.767 0.049 TUBB2A 0.613 0.003 VEGFB 0.780 0.034 ZFP360.576 0.001 ZNF827 0.644 0.014

Analysis of gene expression and upgrading/upstaging was based onunivariate ordinal logistic regression models using weighted maximumlikelihood estimators for each gene in the gene list (727 test genes and5 reference genes). P-values were generated using a Wald test of thenull hypothesis that the odds ratio (OR) is one. Both unadjustedp-values and the q-value (smallest FDR at which the hypothesis test inquestion is rejected) were reported. Un-adjusted p-values<0.05 wereconsidered statistically significant. Since two tumor specimens wereselected for each patient, this analysis was performed using the 2specimens from each patient as follows: (1) analysis using the primaryGleason pattern specimen from each patient (Specimens A1 and B2 asdescribed in Table 2); and (2) analysis using the highest Gleasonpattern specimen from each patient (Specimens A1 and B1 as described inTable 2). 200 genes were found to be significantly associated (p<0.05)with upgrading/upstaging in the primary Gleason pattern sample (PGP) and203 genes were found to be significantly associated (p<0.05) withupgrading/upstaging in the highest Gleason pattern sample (HGP).

Tables 13A and 13B provide genes significantly associated (p<0.05),positively or negatively, with upgrading/upstaging in the primary and/orhighest Gleason pattern. Increased expression of genes in Table 13A ispositively associated with higher risk of upgrading/upstaging (poorprognosis), while increased expression of genes in Table 13B isnegatively associated with risk of upgrading/upstaging (good prognosis).

TABLE 13A Genes significantly (p < 0.05) associated withupgrading/upstaging in the Primary Gleason Pattern (PGP) and HighestGleason Pattern (HGP) OR >1.0 (Increased expression is positivelyassociated with higher risk of upgrading/upstaging (poor prognosis)) PGPHGP Gene OR p-value OR p-value ALCAM 1.52 0.0179 1.50 0.0184 ANLN 1.360.0451 . . APOE 1.42 0.0278 1.50 0.0140 ASPN 1.60 0.0027 2.06 0.0001AURKA 1.47 0.0108 . . AURKB . . 1.52 0.0070 BAX . . 1.48 0.0095 BGN 1.580.0095 1.73 0.0034 BIRC5 1.38 0.0415 . . BMP6 1.51 0.0091 1.59 0.0071BUB1 1.38 0.0471 1.59 0.0068 CACNA1D 1.36 0.0474 1.52 0.0078 CASP7 . .1.32 0.0450 CCNE2 1.54 0.0042 . . CD276 . . 1.44 0.0265 CDC20 1.350.0445 1.39 0.0225 CDKN2B . . 1.36 0.0415 CENPF 1.43 0.0172 1.48 0.0102CLTC 1.59 0.0031 1.57 0.0038 COL1A1 1.58 0.0045 1.75 0.0008 COL3A1 1.450.0143 1.47 0.0131 COL8A1 1.40 0.0292 1.43 0.0258 CRISP3 . . 1.40 0.0256CTHRC1 . . 1.56 0.0092 DBN1 1.43 0.0323 1.45 0.0163 DIAPH1 1.51 0.00881.58 0.0025 DICER1 . . 1.40 0.0293 DIO2 . . 1.49 0.0097 DVL1 . . 1.530.0160 F2R 1.46 0.0346 1.63 0.0024 FAP 1.47 0.0136 1.74 0.0005 FCGR3A .. 1.42 0.0221 HPN . . 1.36 0.0468 HSD17B4 . . 1.47 0.0151 HSPA8 1.650.0060 1.58 0.0074 IL11 1.50 0.0100 1.48 0.0113 IL1B 1.41 0.0359 . .INHBA 1.56 0.0064 1.71 0.0042 KHDRBS3 1.43 0.0219 1.59 0.0045 KIF4A . .1.50 0.0209 KPNA2 1.40 0.0366 . . KRT2 . . 1.37 0.0456 KRT75 . . 1.440.0389 MANF . . 1.39 0.0429 MELK 1.74 0.0016 . . MKI67 1.35 0.0408 . .MMP11 . . 1.56 0.0057 NOX4 1.49 0.0105 1.49 0.0138 PLAUR 1.44 0.0185 . .PLK1 . . 1.41 0.0246 PTK6 . . 1.36 0.0391 RAD51 . . 1.39 0.0300 RAF1 . .1.58 0.0036 RRM2 1.57 0.0080 . . SESN3 1.33 0.0465 . . SFRP4 2.33<0.0001  2.51 0.0015 SKIL 1.44 0.0288 1.40 0.0368 SOX4 1.50 0.0087 1.590.0022 SPINK1 1.52 0.0058 . . SPP1 . . 1.42 0.0224 THBS2 . . 1.36 0.0461TK1 . . 1.38 0.0283 TOP2A 1.85 0.0001 1.66 0.0011 TPD52 1.78 0.0003 1.640.0041 TPX2 1.70 0.0010 . . UBE2G1 1.38 0.0491 . . UBE2T 1.37 0.04251.46 0.0162 UHRF1 . . 1.43 0.0164 VCPIP1 . . 1.37 0.0458

TABLE 13B Genes significantly (p < 0.05) associated withupgrading/upstaging in the Primary Gleason Pattern (PGP) and HighestGleason Pattern (HGP) OR <1.0 (Increased expression is negativelyassociated with higher risk of upgrading/upstaging (good prognosis)) PGPHGP Gene OR p-value OR p-value ABCC3 . . 0.70 0.0216 ABCC8 0.66 0.0121 .. ABCG2 0.67 0.0208 0.61 0.0071 ACE . . 0.73 0.0442 ACOX2 0.46 0.00000.49 0.0001 ADH5 0.69 0.0284 0.59 0.0047 AIG1 . . 0.60 0.0045 AKR1C1 . .0.66 0.0095 ALDH1A2 0.36 <0.0001  0.36 <0.0001  ALKBH3 0.70 0.0281 0.610.0056 ANPEP . . 0.68 0.0109 ANXA2 0.73 0.0411 0.66 0.0080 APC . . 0.680.0223 ATXN1 . . 0.70 0.0188 AXIN2 0.60 0.0072 0.68 0.0204 AZGP1 0.660.0089 0.57 0.0028 BCL2 . . 0.71 0.0182 BIN1 0.55 0.0005 . . BTRC 0.690.0397 0.70 0.0251 C7 0.53 0.0002 0.51 <0.0001  CADM1 0.57 0.0012 0.600.0032 CASP1 0.64 0.0035 0.72 0.0210 CAV1 0.64 0.0097 0.59 0.0032 CAV2 .. 0.58 0.0107 CD164 . . 0.69 0.0260 CD82 0.67 0.0157 0.69 0.0167 CDH10.61 0.0012 0.70 0.0210 CDK14 0.70 0.0354 . . CDK3 . . 0.72 0.0267CDKN1C 0.61 0.0036 0.56 0.0003 CHN1 0.71 0.0214 . . COL6A1 0.62 0.01250.60 0.0050 COL6A3 0.65 0.0080 0.68 0.0181 CSRP1 0.43 0.0001 0.40 0.0002CTSB 0.66 0.0042 0.67 0.0051 CTSD 0.64 0.0355 . . CTSK 0.69 0.0171 . .CTSL1 0.72 0.0402 . . CUL1 0.61 0.0024 0.70 0.0120 CXCL12 0.69 0.02870.63 0.0053 CYP3A5 0.68 0.0099 0.62 0.0026 DDR2 0.68 0.0324 0.62 0.0050DES 0.54 0.0013 0.46 0.0002 DHX9 0.67 0.0164 . . DLGAP1 . . 0.66 0.0086DPP4 0.69 0.0438 0.69 0.0132 DPT 0.59 0.0034 0.51 0.0005 DUSP1 . . 0.670.0214 EDN1 . . 0.66 0.0073 EDNRA 0.66 0.0148 0.54 0.0005 EIF2C2 . .0.65 0.0087 ELK4 0.55 0.0003 0.58 0.0013 ENPP2 0.65 0.0128 0.59 0.0007EPHA3 0.71 0.0397 0.73 0.0455 EPHB2 0.60 0.0014 . . EPHB4 0.73 0.0418 .. EPHX3 . . 0.71 0.0419 ERCC1 0.71 0.0325 . . FAM107A 0.56 0.0008 0.550.0011 FAM13C 0.68 0.0276 0.55 0.0001 FAS 0.72 0.0404 . . FBN1 0.720.0395 . . FBXW7 0.69 0.0417 . . FGF10 0.59 0.0024 0.51 0.0001 FGF7 0.510.0002 0.56 0.0007 FGFR2 0.54 0.0004 0.47 <0.0001  FLNA 0.58 0.0036 0.500.0002 FLNC 0.45 0.0001 0.40 <0.0001  FLT4 0.61 0.0045 . . FOXO1 0.550.0005 0.53 0.0005 FOXP3 0.71 0.0275 0.72 0.0354 GHR 0.59 0.0074 0.530.0001 GNRH1 0.72 0.0386 . . GPM6B 0.59 0.0024 0.52 0.0002 GSN 0.650.0107 0.65 0.0098 GSTM1 0.44 <0.0001  0.43 <0.0001  GSTM2 0.42 <0.0001 0.39 <0.0001  HLF 0.46 <0.0001  0.47 0.0001 HPS1 0.64 0.0069 0.69 0.0134HSPA5 0.68 0.0113 . . HSPB2 0.61 0.0061 0.55 0.0004 HSPG2 0.70 0.0359 .. ID3 . . 0.70 0.0245 IGF1 0.45 <0.0001  0.50 0.0005 IGF2 0.67 0.02000.68 0.0152 IGFBP2 0.59 0.0017 0.69 0.0250 IGFBP6 0.49 <0.0001  0.640.0092 IL6ST 0.56 0.0009 0.60 0.0012 ILK 0.51 0.0010 0.49 0.0004 ITGA10.58 0.0020 0.58 0.0016 ITGA3 0.71 0.0286 0.70 0.0221 ITGA5 . . 0.690.0183 ITGA7 0.56 0.0035 0.42 <0.0001  ITGB1 0.63 0.0095 0.68 0.0267ITGB3 0.62 0.0043 0.62 0.0040 ITPR1 0.62 0.0032 . . JUN 0.73 0.0490 0.680.0152 KIT 0.55 0.0003 0.57 0.0005 KLC1 . . 0.70 0.0248 KLK1 . . 0.600.0059 KRT15 0.58 0.0009 0.45 <0.0001  KRT5 0.70 0.0262 0.59 0.0008LAMA4 0.56 0.0359 0.68 0.0498 LAMB3 . . 0.60 0.0017 LGALS3 0.58 0.00070.56 0.0012 LRP1 0.69 0.0176 . . MAP3K7 0.70 0.0233 0.73 0.0392 MCM30.72 0.0320 . . MMP2 0.66 0.0045 0.60 0.0009 MMP7 0.61 0.0015 0.650.0032 MMP9 0.64 0.0057 0.72 0.0399 MPPED2 0.72 0.0392 0.63 0.0042 MTA1. . 0.68 0.0095 MTSS1 0.58 0.0007 0.71 0.0442 MVP 0.57 0.0003 0.700.0152 MYBPC1 . . 0.70 0.0359 NCAM1 0.63 0.0104 0.64 0.0080 NCAPD3 0.670.0145 0.64 0.0128 NEXN 0.54 0.0004 0.55 0.0003 NFAT5 0.72 0.0320 0.700.0177 NUDT6 0.66 0.0102 . . OLFML3 0.56 0.0035 0.51 0.0011 OMD 0.610.0011 0.73 0.0357 PAGE4 0.42 <0.0001  0.36 <0.0001  PAK6 0.72 0.0335 .. PCDHGB7 0.70 0.0262 0.55 0.0004 PGF 0.72 0.0358 0.71 0.0270 PLP2 0.660.0088 0.63 0.0041 PPAP2B 0.44 <0.0001  0.50 0.0001 PPP1R12A 0.45 0.00010.40 <0.0001  PRIMA1 . . 0.63 0.0102 PRKAR2B 0.71 0.0226 . . PRKCA 0.34<0.0001  0.42 <0.0001  PRKCB 0.66 0.0120 0.49 <0.0001  PROM1 0.61 0.0030. . PTEN 0.59 0.0008 0.55 0.0001 PTGER3 0.67 0.0293 . . PTH1R 0.690.0259 0.71 0.0327 PTK2 0.75 0.0461 . . PTK2B 0.70 0.0244 0.74 0.0388PYCARD 0.73 0.0339 0.67 0.0100 RAD9A 0.64 0.0124 . . RARB 0.67 0.00880.65 0.0116 RGS10 0.70 0.0219 . . RHOB . . 0.72 0.0475 RND3 . . 0.670.0231 SDHC 0.72 0.0443 . . SEC23A 0.66 0.0101 0.53 0.0003 SEMA3A 0.510.0001 0.69 0.0222 SH3RF2 0.55 0.0002 0.54 0.0002 SLC22A3 0.48 0.00010.50 0.0058 SMAD4 0.49 0.0001 0.50 0.0003 SMARCC2 0.59 0.0028 0.650.0052 SMO 0.60 0.0048 0.52 <0.0001  SORBS1 0.56 0.0024 0.48 0.0002SPARCL1 0.43 0.0001 0.50 0.0001 SRD5A2 0.26 <0.0001  0.31 <0.0001  ST50.63 0.0103 0.52 0.0006 STAT5A 0.60 0.0015 0.61 0.0037 STAT5B 0.540.0005 0.57 0.0008 SUMO1 0.65 0.0066 0.66 0.0320 SVIL 0.52 0.0067 0.460.0003 TGFB1I1 0.44 0.0001 0.43 0.0000 TGFB2 0.55 0.0007 0.58 0.0016TGFB3 0.57 0.0010 0.53 0.0005 TIMP1 0.72 0.0224 . . TIMP2 0.68 0.01980.69 0.0206 TIMP3 0.67 0.0105 0.64 0.0065 TMPRSS2 . . 0.72 0.0366TNFRSF10A 0.71 0.0181 . . TNFSF10 0.71 0.0284 . . TOP2B 0.73 0.0432 . .TP63 0.62 0.0014 0.50 <0.0001  TPM1 0.54 0.0007 0.52 0.0002 TPM2 0.41<0.0001  0.40 <0.0001  TPP2 0.65 0.0122 . . TRA2A 0.72 0.0318 . .TRAF3IP2 0.62 0.0064 0.59 0.0053 TRO 0.57 0.0003 0.51 0.0001 VCL 0.520.0005 0.52 0.0004 VIM 0.65 0.0072 0.65 0.0045 WDR19 0.66 0.0097 . .WFDC1 0.58 0.0023 0.60 0.0026 ZFHX3 0.69 0.0144 0.62 0.0046 ZNF827 0.620.0030 0.53 0.0001

Example 3: Identification of MicroRNAs Associated with ClinicalRecurrence and Death Due to Prostate Cancer

MicroRNAs function by binding to portions of messenger RNA (mRNA) andchanging how frequently the mRNA is translated into protein. They canalso influence the turnover of mRNA and thus how long the mRNA remainsintact in the cell. Since microRNAs function primarily as an adjunct tomRNA, this study evaluated the joint prognostic value of microRNAexpression and gene (mRNA) expression. Since the expression of certainmicroRNAs may be a surrogate for expression of genes that are not in theassessed panel, we also evaluated the prognostic value of microRNAexpression by itself.

Patients and Samples

Samples from the 127 patients with clinical recurrence and 374 patientswithout clinical recurrence after radical prostatectomy described inExample 2 were used in this study. The final analysis set comprised 416samples from patients in which both gene expression and microRNAexpression were successfully assayed. Of these, 106 patients exhibitedclinical recurrence and 310 did not have clinical recurrence. Tissuesamples were taken from each prostate sample representing (1) theprimary Gleason pattern in the sample, and (2) the highest Gleasonpattern in the sample. In addition, a sample of histologicallynormal-appearing tissue adjacent to the tumor (NAT) was taken. Thenumber of patients in the analysis set for each tissue type and thenumber of them who experienced clinical recurrence or death due toprostate cancer are shown in Table 14.

TABLE 14 Number of Patients and Events in Analysis Set Clinical DeathsDue to Patients Recurrences Prostate Cancer Primary Gleason 416 106 36Pattern Tumor Tissue Highest Gleason 405 102 36 Pattern Tumor TissueNormal Adjacent Tissue 364 81 29

Assay Method

Expression of 76 test microRNAs and 5 reference microRNAs weredetermined from RNA extracted from fixed paraffin-embedded (FPE) tissue.MicroRNA expression in all three tissue type was quantified by reversetranscriptase polymerase chain reaction (RT-PCR) using the crossingpoint (C_(p)) obtained from the Taqman® MicroRNA Assay kit (AppliedBiosystems, Inc., Carlsbad, Calif.).

Statistical Analysis

Using univariate proportional hazards regression (Cox D R, Journal ofthe Royal Statistical Society, Series B 34:187-220, 1972), applying thesampling weights from the cohort sampling design, and using varianceestimation based on the Lin and Wei method (Lin and Wei, Journal of theAmerican Statistical Association 84:1074-1078, 1989), microRNAexpression, normalized by the average expression for the 5 referencemicroRNAs hsa-miR-106a, hsa-miR-146b-5p, hsa-miR-191, hsa-miR-19b, andhsa-miR-92a, and reference-normalized gene expression of the 733 genes(including the reference genes) discussed above, were assessed forassociation with clinical recurrence and death due to prostate cancer.Standardized hazard ratios (the proportional change in the hazardassociated with a change of one standard deviation in the covariatevalue) were calculated.

This analysis included the following classes of predictors:

1. MicroRNAs alone

2. MicroRNA-gene pairs Tier 1

3. MicroRNA-gene pairs Tier 2

4. MicroRNA-gene pairs Tier 3

5. All other microRNA-gene pairs Tier 4

The four tiers were pre-determined based on the likelihood (Tier 1representing the highest likelihood) that the gene-microRNA pairfunctionally interacted or that the microRNA was related to prostatecancer based on a review of the literature and existing microarray datasets.

False discovery rates (FDR) (Benjamini and Hochberg, Journal of theRoyal Statistical Society, Series B 57:289-300, 1995) were assessedusing Efron's separate class methodology (Efron, Annals of AppliedStatistics 2:197-223., 2008). The false discovery rate is the expectedproportion of the rejected null hypotheses that are rejected incorrectly(and thus are false discoveries). Efron's methodology allows separateFDR assessment (q-values) (Storey, Journal of the Royal StatisticalSociety, Series B 64:479-498, 2002) within each class while utilizingthe data from all the classes to improve the accuracy of thecalculation. In this analysis, the q-value for a microRNA ormicroRNA-gene pair can be interpreted as the empirical Bayes probabilitythat the microRNA or microRNA-gene pair identified as being associatedwith clinical outcome is in fact a false discovery given the data. Theseparate class approach was applied to a true discovery rate degree ofassociation (TDRDA) analysis (Crager, Statistics in Medicine 29:33-45,2010) to determine sets of microRNAs or microRNA-gene pairs that havestandardized hazard ratio for clinical recurrence or prostatecancer-specific death of at least a specified amount while controllingthe FDR at 10%. For each microRNA or microRNA-gene pair, a maximum lowerbound (MLB) standardized hazard ratio was computed, showing the highestlower bound for which the microRNA or microRNA-gene pair was included ina TDRDA set with 10% FDR. Also calculated was an estimate of the truestandardized hazard ratio corrected for regression to the mean (RM) thatoccurs in subsequent studies when the best predictors are selected froma long list (Crager, 2010 above). The RM-corrected estimate of thestandardized hazard ratio is a reasonable estimate of what could beexpected if the selected microRNA or microRNA-gene pair were studied ina separate, subsequent study.

These analyses were repeated adjusting for clinical and pathologycovariates available at the time of patient biopsy: biopsy Gleasonscore, baseline PSA level, and clinical T-stage (T1-T2A vs. T2B or T2C)to assess whether the microRNAs or microRNA-gene pairs have predictivevalue independent of these clinical and pathology covariates.

Results

The analysis identified 21 microRNAs assayed from primary Gleasonpattern tumor tissue that were associated with clinical recurrence ofprostate cancer after radical prostatectomy, allowing a false discoveryrate of 10% (Table 15). Results were similar for microRNAs assessed fromhighest Gleason pattern tumor tissue (Table 16), suggesting that theassociation of microRNA expression with clinical recurrence does notchange markedly depending on the location within a tumor tissue sample.No microRNA assayed from normal adjacent tissue was associated with therisk of clinical recurrence at a false discovery rate of 10%. Thesequences of the microRNAs listed in Tables 15-21 are shown in Table B.

TABLE 15 MicroRNAs Associated with Clinical Recurrence of ProstateCancer Primary Gleason Pattern Tumor Tissue Absolute Standardized HazardRatio q-value^(a) Direction of Uncorrected 95% Confidence Max. LowerRM-Corrected MicroRNA p-value (FDR) Association^(b) Estimate IntervalBound @10% FDR Estimate^(c) hsa-miR-93 <0.0001 0.0% (+) 1.79 (1.38,2.32) 1.19 1.51 hsa-miR-106b <0.0001 0.1% (+) 1.80 (1.38, 2.34) 1.191.51 hsa-miR-30e-5p <0.0001 0.1% (−) 1.63 (1.30, 2.04) 1.18 1.46hsa-miR-21 <0.0001 0.1% (+) 1.66 (1.31, 2.09) 1.18 1.46 hsa-miR-133a<0.0001 0.1% (−) 1.72 (1.33, 2.21) 1.18 1.48 hsa-miR-449a <0.0001 0.1%(+) 1.56 (1.26, 1.92) 1.17 1.42 hsa-miR-30a 0.0001 0.1% (−) 1.56 (1.25,1.94) 1.16 1.41 hsa-miR-182 0.0001 0.2% (+) 1.74 (1.31, 2.31) 1.17 1.45hsa-miR-27a 0.0002 0.2% (+) 1.65 (1.27, 2.14) 1.16 1.43 hsa-miR-2220.0006 0.5% (−) 1.47 (1.18, 1.84) 1.12 1.35 hsa-miR-103 0.0036 2.1% (+)1.77 (1.21, 2.61) 1.12 1.36 hsa-miR-1 0.0037 2.2% (−) 1.32 (1.10, 1.60)1.07 1.26 hsa-miR-145 0.0053 2.9% (−) 1.34 (1.09, 1.65) 1.07 1.27hsa-miR-141 0.0060 3.2% (+) 1.43 (1.11, 1.84) 1.07 1.29 hsa-miR-92a0.0104 4.8% (+) 1.32 (1.07, 1.64) 1.05 1.25 hsa-miR-22 0.0204 7.7% (+)1.31 (1.03, 1.64) 1.03 1.23 hsa-miR-29b 0.0212 7.9% (+) 1.36 (1.03,1.76) 1.03 1.24 hsa-miR-210 0.0223 8.2% (+) 1.33 (1.03, 1.70) 1.00 1.23hsa-miR-486-5p 0.0267 9.4% (−) 1.25 (1.00, 1.53) 1.00 1.20 hsa-miR-19b0.0280 9.7% (−) 1.24 (1.00, 1.50) 1.00 1.19 hsa-miR-205 0.0289 10.0% (−)1.25 (1.00, 1.53) 1.00 1.20 ^(a)The q-value is the empirical Bayesprobability that the microRNA's association with clinical recurrence isa false discovery, given the data. ^(b)Direction of associationindicates where higher microRNA expression is associated with higher (+)or lower (−) risk of clinical recurrence. ^(c)RM: regression to themean.

TABLE 16 MicroRNAs Associated with Clinical Recurrence of ProstateCancer Highest Gleason Pattern Tumor Tissue Absolute Standardized HazardRatio q-value^(a) Direction of Uncorrected 95% Confidence Max. LowerRM-Corrected MicroRNA p-value (FDR) Association^(b) Estimate IntervalBound @10% FDR Estimate^(c) hsa-miR-93 <0.0001 0.0% (+) 1.91 (1.48,2.47) 1.24 1.59 hsa-miR-449a <0.0001 0.0% (+) 1.75 (1.40, 2.18) 1.231.54 hsa-miR-205 <0.0001 0.0% (−) 1.53 (1.29, 1.81) 1.20 1.43hsa-miR-19b <0.0001 0.0% (−) 1.37 (1.19, 1.57) 1.15 1.32 hsa-miR-106b<0.0001 0.0% (+) 1.84 (1.39, 2.42) 1.22 1.51 hsa-miR-21 <0.0001 0.0% (+)1.68 (1.32, 2.15) 1.19 1.46 hsa-miR-30a 0.0005 0.4% (−) 1.44 (1.17,1.76) 1.13 1.33 hsa-miR-30e-5p 0.0010 0.6% (−) 1.37 (1.14, 1.66) 1.111.30 hsa-miR-133a 0.0015 0.8% (−) 1.57 (1.19, 2.07) 1.13 1.36 hsa-miR-10.0016 0.8% (−) 1.42 (1.14, 1.77) 1.11 1.31 hsa-miR-103 0.0021 1.1% (+)1.69 (1.21, 2.37) 1.13 1.37 hsa-miR-210 0.0024 1.2% (+) 1.43 (1.13,1.79) 1.11 1.31 hsa-miR-182 0.0040 1.7% (+) 1.48 (1.13, 1.93) 1.11 1.31hsa-miR-27a 0.0055 2.1% (+) 1.46 (1.12, 1.91) 1.09 1.30 hsa-miR-2220.0093 3.2% (−) 1.38 (1.08, 1.77) 1.08 1.27 hsa-miR-331 0.0126 3.9% (+)1.38 (1.07, 1.77) 1.07 1.26 hsa-miR-191* 0.0143 4.3% (+) 1.38 (1.06,1.78) 1.07 1.26 hsa-miR-425 0.0151 4.5% (+) 1.40 (1.06, 1.83) 1.07 1.26hsa-miR-31 0.0176 5.1% (−) 1.29 (1.04, 1.60) 1.05 1.22 hsa-miR-92a0.0202 5.6% (+) 1.31 (1.03, 1.65) 1.05 1.23 hsa-miR-155 0.0302 7.6% (−)1.32 (1.00, 1.69) 1.03 1.22 hsa-miR-22 0.0437 9.9% (+) 1.30 (1.00, 1.67)1.00 1.21 ^(a)The q-value is the empirical Bayes probability that themicroRNA's association with death due to prostate cancer is a falsediscovery, given the data. ^(b)Direction of association indicates wherehigher microRNA expression is associated with higher (+) or lower (−)risk of clinical recurrence. ^(c)RM: regression to the mean.

Table 17 shows microRNAs assayed from primary Gleason pattern tissuethat were identified as being associated with the risk ofprostate-cancer-specific death, with a false discovery rate of 10%.Table 18 shows the corresponding analysis for microRNAs assayed fromhighest Gleason pattern tissue. No microRNA assayed from normal adjacenttissue was associated with the risk of prostate-cancer-specific death ata false discovery rate of 10%.

TABLE 17 MicroRNAs Associated with Death Due to Prostate Cancer PrimaryGleason Pattern Tumor Tissue Absolute Standardized Hazard Ratioq-value^(a) Direction of Uncorrected 95% Confidence Max. LowerRM-Corrected MicroRNA p-value (FDR) Association^(b) Estimate IntervalBound @10% FDR Estimate^(c) hsa-miR-30e-5p 0.0001 0.6% (−) 1.88 (1.37,2.58) 1.15 1.46 hsa-miR-30a 0.0001 0.7% (−) 1.78 (1.33, 2.40) 1.14 1.44hsa-miR-133a 0.0005 1.2% (−) 1.85 (1.31, 2.62) 1.13 1.41 hsa-miR-2220.0006 1.4% (−) 1.65 (1.24, 2.20) 1.12 1.38 hsa-miR-106b 0.0024 2.7% (+)1.85 (1.24, 2.75) 1.11 1.35 hsa-miR-1 0.0028 3.0% (−) 1.43 (1.13, 1.81)1.08 1.30 hsa-miR-21 0.0034 3.3% (+) 1.63 (1.17, 2.25) 1.09 1.33hsa-miR-93 0.0044 3.9% (+) 1.87 (1.21, 2.87) 1.09 1.32 hsa-miR-26a0.0072 5.3% (−) 1.47 (1.11, 1.94) 1.07 1.29 hsa-miR-152 0.0090 6.0% (−)1.46 (1.10, 1.95) 1.06 1.28 hsa-miR-331 0.0105 6.5% (+) 1.46 (1.09,1.96) 1.05 1.27 hsa-miR-150 0.0159 8.3% (+) 1.51 (1.07, 2.10) 1.03 1.27hsa-miR-27b 0.0160 8.3% (+) 1.97 (1.12, 3.42) 1.05 1.25 ^(a)The q-valueis the empirical Bayes probability that the microRNA's association withdeath due to prostate cancer endpoint is a false discovery, given thedata. ^(b)Direction of association indicates where higher microRNAexpression is associated with higher (+) or lower (−) risk of death dueto prostate cancer. ^(c)RM: regression to the mean.

TABLE 18 MicroRNAs Associated with Death Due to Prostate Cancer HighestGleason Pattern Tumor Tissue Absolute Standardized Hazard Ratioq-value^(a) Direction of Uncorrected 95% Confidence Max. LowerRM-Corrected MicroRNA p-value (FDR) Association^(b) Estimate IntervalBound @10% FDR Estimate^(c) hsa-miR-27b 0.0016 6.1% (+) 2.66 (1.45,4.88) 1.07 1.32 hsa-miR-21 0.0020 6.4% (+) 1.66 (1.21, 2.30) 1.05 1.34hsa-miR-10a 0.0024 6.7% (+) 1.78 (1.23, 2.59) 1.05 1.34 hsa-miR-930.0024 6.7% (+) 1.83 (1.24, 2.71) 1.05 1.34 hsa-miR-106b 0.0028 6.8% (+)1.79 (1.22, 2.63) 1.05 1.33 hsa-miR-150 0.0035 7.1% (+) 1.61 (1.17,2.22) 1.05 1.32 hsa-miR-1 0.0104 9.0% (−) 1.52 (1.10, 2.09) 1.00 1.28^(a)The q-value is the empirical Bayes probability that the microRNA'sassociation with clinical endpoint is a false discovery, given the data.^(b)Direction of association indicates where higher microRNA expressionis associated with higher (+) or lower (−) risk of death due to prostatecancer. ^(c)RM: regression to the mean.

Table 19 and Table 20 shows the microRNAs that can be identified asbeing associated with the risk of clinical recurrence while adjustingfor the clinical and pathology covariates of biopsy Gleason score,baseline PSA level, and clinical T-stage. The distributions of thesecovariates are shown in FIG. 1 . Fifteen (15) of the microRNAsidentified in Table 15 are also present in Table 19, indicating thatthese microRNAs have predictive value for clinical recurrence that isindependent of the Gleason score, baseline PSA, and clinical T-stage.

Two microRNAs assayed from primary Gleason pattern tumor tissue werefound that had predictive value for death due to prostate cancerindependent of Gleason score, baseline PSA, and clinical T-stage (Table21).

TABLE 19 MicroRNAs Associated with Clinical Recurrence of ProstateCancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, andClinical T-Stage Primary Gleason Pattern Tumor Tissue AbsoluteStandardized Hazard Ratio q-value^(a) Direction of Uncorrected 95%Confidence Max. Lower RM-Corrected MicroRNA p-value (FDR)Association^(b) Estimate Interval Bound @10% FDR Estimate^(c)hsa-miR-30e-5p <0.0001 0.0% (−) 1.80 (1.42, 2.27) 1.23 1.53 hsa-miR-30a<0.0001 0.0% (−) 1.75 (1.40, 2.19) 1.22 1.51 hsa-miR-93 <0.0001 0.1% (+)1.70 (1.32, 2.20) 1.19 1.44 hsa-miR-449a 0.0001 0.1% (+) 1.54 (1.25,1.91) 1.17 1.39 hsa-miR-133a 0.0001 0.1% (−) 1.58 (1.25, 2.00) 1.17 1.39hsa-miR-27a 0.0002 0.1% (+) 1.66 (1.28, 2.16) 1.17 1.41 hsa-miR-210.0003 0.2% (+) 1.58 (1.23, 2.02) 1.16 1.38 hsa-miR-182 0.0005 0.3% (+)1.56 (1.22, 1.99) 1.15 1.37 hsa-miR-106b 0.0008 0.5% (+) 1.57 (1.21,2.05) 1.15 1.36 hsa-miR-222 0.0028 1.1% (−) 1.39 (1.12, 1.73) 1.11 1.28hsa-miR-103 0.0048 1.7% (+) 1.69 (1.17, 2.43) 1.13 1.32 hsa-miR-486-5p0.0059 2.0% (−) 1.34 (1.09, 1.65) 1.09 1.25 hsa-miR-1 0.0083 2.7% (−)1.29 (1.07, 1.57) 1.07 1.23 hsa-miR-141 0.0088 2.8% (+) 1.43 (1.09,1.87) 1.09 1.27 hsa-miR-200c 0.0116 3.4% (+) 1.39 (1.07, 1.79) 1.07 1.25hsa-miR-145 0.0201 5.1% (−) 1.27 (1.03, 1.55) 1.05 1.20 hsa-miR-2060.0329 7.2% (−) 1.40 (1.00, 1.91) 1.05 1.23 hsa-miR-29b 0.0476 9.4% (+)1.30 (1.00, 1.69) 1.00 1.20 ^(a)The q-value is the empirical Bayesprobability that the microRNA's association with clinical recurrence isa false discovery, given the data. ^(b)Direction of associationindicates where higher microRNA expression is associated with higher (+)or lower (−) risk of clinical recurrence. ^(c)RM: regression to themean.

TABLE 20 MicroRNAs Associated with Clinical Recurrence of ProstateCancer Adjusting for Biopsy Gleason Score, Baseline PSA Level, andClinical T-Stage Highest Gleason Pattern Tumor Tissue AbsoluteStandardized Hazard Ratio q-value^(a) Direction of Uncorrected 95%Confidence Max. Lower RM-Corrected MicroRNA p-value (FDR)Association^(b) Estimate Interval Bound @10% FDR Estimate^(c)hsa-miR-30a <0.0001 0.0% (−) 1.62 (1.32, 1.99) 1.20 1.43 hsa-miR-30e-5p<0.0001 0.0% (−) 1.53 (1.27, 1.85) 1.19 1.39 hsa-miR-93 <0.0001 0.0% (+)1.76 (1.37, 2.26) 1.20 1.45 hsa-miR-205 <0.0001 0.0% (−) 1.47 (1.23,1.74) 1.18 1.36 hsa-miR-449a 0.0001 0.1% (+) 1.62 (1.27, 2.07) 1.18 1.38hsa-miR-106b 0.0003 0.2% (+) 1.65 (1.26, 2.16) 1.17 1.36 hsa-miR-133a0.0005 0.2% (−) 1.51 (1.20, 1.90) 1.16 1.33 hsa-miR-1 0.0007 0.3% (−)1.38 (1.15, 1.67) 1.13 1.28 hsa-miR-210 0.0045 1.2% (+) 1.35 (1.10,1.67) 1.11 1.25 hsa-miR-182 0.0052 1.3% (+) 1.40 (1.10, 1.77) 1.11 1.26hsa-miR-425 0.0066 1.6% (+) 1.48 (1.12, 1.96) 1.12 1.26 hsa-miR-1550.0073 1.8% (−) 1.36 (1.09, 1.70) 1.10 1.24 hsa-miR-21 0.0091 2.1% (+)1.42 (1.09, 1.84) 1.10 1.25 hsa-miR-222 0.0125 2.7% (−) 1.34 (1.06,1.69) 1.09 1.23 hsa-miR-27a 0.0132 2.8% (+) 1.40 (1.07, 1.84) 1.09 1.23hsa-miR-191* 0.0150 3.0% (+) 1.37 (1.06, 1.76) 1.09 1.23 hsa-miR-1030.0180 3.4% (+) 1.45 (1.06, 1.98) 1.09 1.23 hsa-miR-31 0.0252 4.3% (−)1.27 (1.00, 1.57) 1.07 1.19 hsa-miR-19b 0.0266 4.5% (−) 1.29 (1.00,1.63) 1.07 1.20 hsa-miR-99a 0.0310 5.0% (−) 1.26 (1.00, 1.56) 1.06 1.18hsa-miR-92a 0.0348 5.4% (+) 1.31 (1.00, 1.69) 1.06 1.19 hsa-miR-146b-5p0.0386 5.8% (−) 1.29 (1.00, 1.65) 1.06 1.19 hsa-miR-145 0.0787 9.7% (−)1.23 (1.00, 1.55) 1.00 1.15 ^(a)The q-value is the empirical Bayesprobability that the microRNA's association with clinical clinicalrecurrence is a false discovery, given the data. ^(b)Direction ofassociation indicates where higher microRNA expression is associatedwith higher (+) or lower (−) risk of clinical recurrence. ^(c)RM:regression to the mean.

TABLE 21 MicroRNAs Associated with Death Due to Prostate CancerAdjusting for Biopsy Gleason Score, Baseline PSA Level, and ClinicalT-Stage Primary Gleason Pattern Tumor Tissue Absolute StandardizedHazard Ratio q-value^(a) Direction of Uncorrected 95% Confidence Max.Lower RM-Corrected MicroRNA p-value (FDR) Association^(b) EstimateInterval Bound @10% FDR Estimate^(c) hsa-miR-30e-5p 0.0001 2.9% (−) 1.97(1.40, 2.78) 1.09 1.39 hsa-miR-30a 0.0002 3.3% (−) 1.90 (1.36, 2.65)1.08 1.38 ^(a)The q-value is the empirical Bayes probability that themicroRNA's association with clinical recurrence is a false discovery,given the data. ^(b)Direction of association indicates where highermicroRNA expression is associated with higher (+) or lower (−) risk ofclinical recurrence. ^(c)RM: regression to the mean.

Accordingly, the normalized expression levels of hsa-miR-93;hsa-miR-106b; hsa-miR-21; hsa-miR-449a; hsa-miR-182; hsa-miR-27a;hsa-miR-103; hsa-miR-141; hsa-miR-92a; hsa-miR-22; hsa-miR-29b;hsa-miR-210; hsa-miR-331; hsa-miR-191; hsa-miR-425; and hsa-miR-200c arepositively associated with an increased risk of recurrence; andhsa-miR-30e-5p; hsa-miR-133a; hsa-miR-30a; hsa-miR-222; hsa-miR-1;hsa-miR-145; hsa-miR-486-5p; hsa-miR-19b; hsa-miR-205; hsa-miR-31;hsa-miR-155; hsa-miR-206; hsa-miR-99a; and hsa-miR-146b-5p arenegatively associated with an increased risk of recurrence.

Furthermore, the normalized expression levels of hsa-miR-106b;hsa-miR-21; hsa-miR-93; hsa-miR-331; hsa-miR-150; hsa-miR-27b; andhsa-miR-10a are positively associated with an increased risk of prostatecancer specific death; and the normalized expression levels ofhsa-miR-30e-5p; hsa-miR-30a; hsa-miR-133a; hsa-miR-222; hsa-miR-1;hsa-miR-26a; and hsa-miR-152 are negatively associated with an increasedrisk of prostate cancer specific death.

Table 22 shows the number of microRNA-gene pairs that were grouped ineach tier (Tiers 1-4) and the number and percentage of those that werepredictive of clinical recurrence at a false discovery rate of 10%.

TABLE 22 Number of Pairs Predictive Total Number of of ClinicalRecurrence at Tier MicroRNA-Gene Pairs False Discovery Rate 10% (%) Tier1 80 46 (57.5%) Tier 2 719 591 (82.2%) Tier 3 3,850 2,792 (72.5%) Tier 454,724 38,264 (69.9%)

TABLE A SEQ SEQ SEQ SEQ Official Accession ID Forward ID Reverse ID IDSymbol: Number: NO Primer Sequence: NO Primer Sequence: NOProbe Sequence: NO Amplicon Sequence: AAMP NM_001087 1GTGTGGCAGGTGGACACTAA 2 CTCCATCCACTCCAGGTCTC 3 CGCTTCAAAGGACCAGACCTCCTC 4GTGTGGCAGGTGGACACTAAGGAGGAGGTCTGGTCCTT TGAAGCGGGAGACCTGGAGTGGATGGAGABCA5 NM_172232 5 GGTATGGATCCCAAAGCCA 6 CAGCCCGCTTTCTGTTTTTA 7CACATGTGGCGAGCAATTCGAACT 8 GGTATGGATCCCAAAGCCAAACAGCACATGTGGCGAGCAATTCGAACTGCATTTAAAAACAGAAAGCGGGCTG ABCB1 NM_000927 9AAACACCACTGGAGCATTGA 10 CAAGCCTGGAACCTATAGCC 11 CAAGCCTGGAACCTATAGCC 12AAACACCACTGGAGCATTGACTACCAGGCTCGCCAATGATGCTGCTCAAGTTAAAGGGGCTATAGGTTCCAGGCTT G ABCC1 NM_004996 13TCATGGTGCCCGTCAATG 14 CGATTGTCTTTGCTCTTCAT 15 ACCTGATACGTCTTGGTCTTCATC16 TCATGGTGCCCGTCAATGCTGTGATGGCGATGAAGACC GTG GCCATAAGACGTATCAGGTGGCCCACATGAAGAGCAAAGACAA TCG ABCC3 NM_003786 17TCATCCTGGCGATCTACTTC 18 CCGTTGAGTGGAATCAGCAA 19 TCTGTCCTGGCTGGAGTCGCTTTC20 TCATCCTGGCGATCTACTTCCTCTGGCAGAACCTAGGT CT ATCCCTCTGTCCTGGCTGGAGTCGCTTTCATGGTCTTGCT GATTCCACTCAACGG ABCC4 NM_00584521 AGCGCCTGGAATCTACAACT 22 AGAGCCCCTGGAGAGAAGAT 23CGGAGTCCAGTGTTTTCCCACTTA 24 AGCGCCTGGAATCTACAACTCGGAGTCCAGTGTTTTCCCACTTATCATCTTCTCTCCAGGGGCTCT ABCC8 NM_000352 25 CGTCTGTCACTGTGGAGTGG 26TGATCCGGTTTAGCAGGC 27 AGTCTCTTGGCCACCTTCAGCCCT 28CGTCTGTCACTGTGGAGTGGACAGGGCTGAAGGTGGCCAAGAGACTGCACCGCAGCCTGCTAAACCGGATCA ABCG2 NM_004827 29 GGTCTCAACGCCATCCTG30 CTTGGATCTTTCCTTGCAGC 31 ACGAAGATTTGCCTCCACCTGTGG 32GGTCTCAACGCCATCCTGGGACCCACAGGTGGAGGCAAATCTTCGTTATTAGATGTCTTAGCTGCAAGGAAAGATC CAAG ABHD2 NM_007011 33GTAGTGGGTCTGCATGGATG 34 TGAGGGTTGGCACTCAGG 35 CAGGTGGCTCCTTTGATCCCTGA 36GTAGTGGGTCTGCATGGATGTTTCAGGGATCAAAGGAG T CCACCTGGGCGCCTGAGTGCCAACCCTCAACE NM_000789 37 CCGCTGTACGAGGATTTCA 38 CCGTGTCTGTGAAGCCGT 39TGCCCTCAGCAATGAAGCCTACAA 40 CCGCTGTACGAGGATTTCACTGCCCTCAGCAATGAAGCCTACAAGCAGGACGGCTTCACAGACACGG ACOX2 NM_003500 41 ATGGAGGTGCCCAGAACAC 42ACTCCGGGTAACTGTGGATG 43 TGCTCTCAACTTTCCTGCGGAGTG 44ATGGAGGTGCCCAGAACACTGCACTCCGCAGGAAAGTT GAGAGCATCATCCACAGTTACCCGGAGTACTR2 NM_005722 45 ATCCGCATTGAAGACCCA 46 ATCCGCTAGAACTGCACCAC 47CCCGCAGAAAGCACATGGTATTCC 48 ATCCGCATTGAAGACCCACCCCGCAGAAAGCACATGGTATTCCTGGGTGGTGCAGTTCTAGCGGAT ADAM15 NM_003815 49 GGCGGGATGTGGTAACAG 50ATTTCTGGGCCTCCGAGT 51 TCAGCCACAATCACCAACTCCACA 52GGCGGGATGTGGTAACAGAGACCAAGACTGTGGAGTTGGTGATTGTGGCTGATCACTCGGAGGCCCAGAAAT ADAMTS1 NM_006988 53GGACAGGTGCAAGCTCATCTG 54 ATCTACAACCTTGGGCTGCA 55CAAGCCAAAGGCATTGGCTACTTC 56 GGACAGGTGCAAGCTCATCTGCCAAGCCAAAGGCATTG ATTCG GCTACTTCTTCGTTTTGCAGCCCAAGGTTGTAGAT ADH5 NM_000671 57ATGCTGTCATCATTGTCACG 58 CTGCTTCCTTTCCCTTTCC 59 TGTCTGCCCATTATCTTCATTCTG60 ATGCTGTCATCATTGTCACGGTTTGTCTGCCCATTATC CAATTCATTCTGCAAGGGAAAGGGAAAGGAAGCAG AFAP1 NM_198595 61GATGTCCATCCTTGAAACAGC 62 CAACCCTGATGCCTGGAG 63 CCTCCAGTGCTGTGTTCCCAGAAG64 GATGTCCATCCTTGAAACAGCCTCTTCTGGGAACACAG CACTGGAGGTCTCCAGGCATCAGGGTTGAGTR1 NM_000685 65 AGCATTGATCGATACCTGGC 66 CTACAAGCATTGTGCGTCG 67ATTGTTCACCCAATGAAGTCCCGC 68 AGCATTGATCGATACCTGGCTATTGTTCACCCAATGAAGTCCCGCCTTCGACGCACAATGCTTGTAG AGTR2 NM_000686 69 ACTGGCATAGGAAATGGTATC70 ATTGACTGGGTCTCTTTGCC 71 CCACCCAGACCCCATGTAGCAAAA 72ACTGGCATAGGAAATGGTATCCAGAATGGAATTTTGCT CACATGGGGTCTGGGTGGGGGCAAAGAGACCCAGTCAAT AIG1 NM_016108 73CGACGGTTCTGCCCTTTAT 74 TGCTCCTGCTGGGATACTG 75 AATCGAGATGAGGACATCGCACCA76 CGACGGTTCTGCCCTTTATATTAATCGAGATGAGGACA TCGCACCATCAGTATCCCAGCAGGAGCAAKAP1 NM_003488 77 TGTGGTTGGAGATGAAGTGG 78 GTCTACCCACTGGGCAAGG 79CTCCACCAGGGACCGGTTTATCAA 80 TGTGGTTGGAGATGAAGTGGTGTTGATAAACCGGTCCCTGGTGGAGCGAGGCCTTGCCCAGTGGGTAGAC AKR1C1 BC040210 81GTGTGTGAAGCTGAATGATGG 82 CTCTGCAGGCGCATAGGT 83 CCAAATCCCAGGACAGGCATGAAG84 GTGTGTGAAGCTGAATGATGGTCACTTCATGCCTGTCC TGGGATTTGGCACCTATGCGCCTGCAGAGAKR1C3 NM_003739 85 GCTTTGCCTGATGTCTACCAG 86 GTCCAGTCACCGGCATAGAG 87TGCGTCACCATCCACACACAGGG 88 GCTTTGCCTGATGTCTACCAGAAGCCCTGTGTGTGGAT AA AGGTGACGCAGAGGACGTCTCTATGCCGGTGACTGGAC AKT1 NM_005163 89CGCTTCTATGGCGCTGAGAT 90 TCCCGGTACACCACGTTCTT 91 CAGCCCTGGACTACCTGCACTCGG92 CGCTTCTATGGCGCTGAGATTGTGTCAGCCCTGGACTACCTGCACTCGGAGAAGAACGTGGTGTACCGGGA AKT2 NM_001626 93 TCCTGCCACCCTTCAAACC94 GGCGGTAAATTCATCATCGA 95 CAGGTCACGTCCGAGGTCGACACA 96TCCTGCCACCCTTCAAACCTCAGGTCACGTCCGAGGTC AGACACAAGGTACTTCGATGATGAATTTACCGCC AKT3 NM_005465 97TTGTCTCTGCCTTGGACTATC 98 CCAGCATTAGATTCTCCAAC 99 TCACGGTACACAATCTTTCCGGA100 TTGTCTCTGCCTTGGACTATCTACATTCCGGAAAGATT TACA TTGAGTGTACCGTGATCTCAAGTTGGAGAATCTAATGCTGG ALCAM NM_001627 101GAGGAATATGGAATCCAAGGG 102 GTGGCGGAGATCAAGAGG 103CCAGTTCCTGCCGTCTGCTCTTCT 104 GAGGAATATGGAATCCAAGGGGGCCAGTTCCTGCCGTCTGCTCTTCTGCCTCTTGATCTCCGCCAC ALDH18A1 NM_002860 105 GATGCAGCTGGAACCCAA106 CTCCAGCTCAGTGGGGAA 107 CCTGAAACTTGCATCTCCTGCTGC 108GATGCAGCTGGAACCCAAGCTGCAGCAGGAGATGCAAG TTTCAGGATGTTCCCCACTGAGCTGGAGALDH1A2 NM_170696 109 CACGTCTGTCCCTCTCTGCT 110 GACCGTGGCTCAACTTTGTA 111TCTCTGTAGGGCCCAGCTCTCAGG 112 CACGTCTGTCCCTCTCTGCTTTCTCTGTAGGGCCCAGC TTCTCAGGAATACAAAGTTGAGCCACGGTC ALKBH3 NM_139178 113 TCGCTTAGTCTGCACCTCAAC114 TCTGAGCCCCAGTTTTTCC 115 TAAACAGGGCAGTCACTTTCCGCA 116TCGCTTAGTCTGCACCTCAACCGTGCGGAAAGTGACTG CCCTGTTTACTGAGGAAAAACTGGGGCTCAGAALOX12 NM_000697 117 AGTTCCTCAATGGTGCCAAC 118 AGCACTAGCCTGGAGGGC 119CATGCTGTTGAGACGCTCGACCTC 120 AGTTCCTCAATGGTGCCAACCCCATGCTGTTGAGACGCTCGACCTCTCTGCCCTCCAGGCTAGTGCT ALOX5 NM_000698 121 GAGCTGCAGGACTTCGTGA122 GAAGCCTGAGGACTTGCG 123 CCGCATGCCGTACACGTAGACATC 124GAGCTGCAGGACTTCGTGAACGATGTCTACGTGTACGG CATGCGGGGCCGCAAGTCCTCAGGCTTCAMACR NM_203382 125 GTCTCTGGGCTGTCAGCTTT 126 TGGGTATAAGATCCAGAACT 127TCCATGTGTTTGATTTCTCCTCAG 128 GTCTCTGGGCTGTCAGCTTTCCTTTCTCCATGTGTTTG TGCGC ATTTCTCCTCAGGCTGGTAGCAAGTTCTGGATCTTATA CCCA AMPD3 NM_000480 129TGGTTCATCCAGCACAAGG 130 CATAAATCCGGGGCACCT 131 TACTCTCCCAACATGCGCTGGATC132 TGGTTCATCCAGCACAAGGTCTACTCTCCCAACATGCG CTGGATCATCCAGGTGCCCCGGATTTATGANGPT2 NM_001147 133 CCGTGAAAGCTGCTCTGTAA 134 TTGCAGTGGGAAGAACAGTC 135AAGCTGACACAGCCCTCCCAAGTG 136 CCGTGAAAGCTGCTCTGTAAAAGCTGACACAGCCCTCCCAAGTGAGCAGGACTGTTCTTCCCACTGCAA ANLN NM_018685 137 TGAAAGTCCAAAACCAGGAA138 CAGAACCAAGGCTATCACCA 139 CCAAAGAACTCGTGTCCCTCGAGC 140TGAAAGTCCAAAACCAGGAAAATTCCAAAGAACTCGTGTCCCTCGAGCTGAATCTGGTGATAGCCTTGGTTCTG ANPEP NM_001150 141CCACCTTGGACCAAAGTAAAG 142 TCTCAGCGTCACCTGGTAGG 143CTCCCCAACACGCTGAAACCCG 144 CCACCTTGGACCAAAGTAAAGCGTGGAATCGTTACCGC C ACTCCCCAACACGCTGAAACCCGATTCCTACCGGGTGAC GCTGAGA ANXA2 NM_004039 145CAAGACACTAAGGGCGACTAC 146 CGTGTCGGGCTTCAGTCAT 147CCACCACACAGGTACAGCAGCGCT 148 CAAGACACTAAGGGCGACTACCAGAAAGCGCTGCTGTA CACCTGTGTGGTGGAGATGACTGAAGCCCGACACG APC NM_000038 149 GGACAGCAGGAATGTGTTTC150 ACCCACTCGATTTGTTTCTG 151 CATTGGCTCCCCGTGACCTGTA 152GGACAGCAGGAATGTGTTTCTCCATACAGGTCACGGGG AGCCAATGGTTCAGAAACAAATCGAGTGGGTAPEX1 NM_001641 153 GATGAAGCCTTTCGCAAGTT 154 AGGTCTCCACACAGCACAAG 155CTTTCGGGAAGCCAGGCCCTT 156 GATGAAGCCTTTCGCAAGTTCCTGAAGGGCCTGGCTTCCCGAAAGCCCCTTGTGCTGTGTGGAGACCT APOC1 NM_001645 157 CCAGCCTGATAAAGGTCCTG158 CACTCTGAATCCTTGCTGGA 159 AGGACAGGACCTCCCAACCAAGC 160CCAGCCTGATAAAGGTCCTGCGGGCAGGACAGGACCTC CCAACCAAGCCCTCCAGCAAGGATTCAGAGTGAPOE NM_000041 161 GCCTCAAGAGCTGGTTCG 162 CCTGCACCTTCTCCACCA 163ACTGGCGCTGCATGTCTTCCAC 164 GCCTCAAGAGCTGGTTCGAGCCCCTGGTGGAAGACATGCAGCGCCAGTGGGCCGGGCTGGTGGAGAAGGTGCAGG APRT NM_000485 165GAGGTCCTGGAGTGCGTG 166 AGGTGCCAGCTTCTCCCT 167 CCTTAAGCGAGGTCAGCTCCACCA168 GAGGTCCTGGAGTGCGTGAGCCTGGTGGAGCTGACCTC GCTTAAGGGCAGGGAGAAGCTGGCACCTAQP2 NM_000486 169 GTGTGGGTGCCAGTCCTC 170 CCCTTCAGCCCTCTCAAAG 171CTCCTTCCCTTCCCCTTCTCCTGA 172 GTGTGGGTGCCAGTCCTCCTCAGGAGAAGGGGAAGGGAAGGAGGCCACTTTGAGAGGGCTGAAGGG AR NM_000044 173 CGACTTCACCGCACCTGAT 174TGACACAAGTGGGACTGGGA 175 ACCATGCCGCCAGGGTACCACA 176CGACTTCACCGCACCTGATGTGTGGTACCCTGGCGGCA TATGGTGAGCAGAGTGCCCTATCCCAGTCCCACTTGTGTC A ARF1 NM_001658 177CAGTAGAGATCCCCGCAACT 178 ACAAGCACATGGCTATGGAA 179 CTTGTCCTTGGGTCACCCTGCA180 CAGTAGAGATCCCCGCAACTCGCTTGTCCTTGGGTCAC CCTGCATTCCATAGCCATGTGCTTGTARHGAP29 NM_004815 181 CACGGTCTCGTGGTGAAGT 182 CAGTTGCTTGCCCAGGAC 183ATGCCAGACCCAGACAAAGCATCA 184 CACGGTCTCGTGGTGAAGTCAATGCCAGACCCAGACAAAGCATCAGCTTGTCCTGGGCAAGCAACTG ARHGDIB NM_001175 185 TGGTCCCTAGAACAAGAGGC186 TGATGGAGGATCAGAGGGAG 187 TAAAACCGGGCTTTCACCCAACCT 188TGGTCCCTAGAACAAGAGGCTTAAAACCGGGCTTTCAC CCAACCTGCTCCCTCTGATCCTCCATCAASAP2 NM_003887 189 CGGCCCATCAGCTTCTAC 190 CTCTGGCCAAAGATACAGCG 191CTGGGCTCCAACCAGCTTCAGTCT 192 CGGCCCATCAGCTTCTACCAGCTGGGCTCCAACCAGCTTCAGTCTAACGCTGTATCTTTGGCCAGAG ASPN NM_017680 193 TGGACTAATCTGTGGGAGCA194 AAACACCCTTCAACACAGTC 195 AGTATCACCCAGGGTGCAGCCAC 196TGGACTAATCTGTGGGAGCAGTTTATTCCAGTATCACC CCAGGGTGCAGCCACACCAGGACTGTGTTGAAGGGTGTT T ATM NM_000051 197TGCTTTCTACACATGTTCAGG 198 GTTGTGGATCGGCTCGTT 199CCAGCTGTCTTCGACACTTCTCGC 200 TGCTTTCTACACATGTTCAGGGATTTTTCACCAGCTGT GCTTCGACACTTCTCGCAAACGAGCCGATCCACAAC ATP5E NM_006886 201CCGCTTTCGCTACAGCAT 202 TGGGAGTATCGGATGTAGCT 203 TCCAGCCTGTCTCCAGTAGGCCAC204 CCGCTTTCGCTACAGCATGGTGGCCTACTGGAGACAGG GCTGGACTCAGCTACATCCGATACTCCCA ATP5J NM_001003703 205 GTCGACCGACTGAAACGG206 CTCTACTTCCGGCCCTGG 207 CTACCCGCCATCGCAATGCATTAT 208GTCGACCGACTGAAACGGCGGCCCATAATGCATTGCGATGGCGGGTAGGCGTGTGGGGGCGGAGCCAGGGCCGGAA GTAGAG ATXN1 NM_000332 209GATCGACTCCAGCACCGTAG 210 GAACTGTATCACGGCCACG 211CGGGCTATGGCTGTCTTCAATCCT 212 GATCGACTCCAGCACCGTAGAGAGGATTGAAGACAGCCATAGCCCGGGCGTGGCCGTGATACAGTTC AURKA NM_003600 213 CATCTTCCAGGAGGACCACT214 TCCGACCTTCAATCATTTCA 215 CTCTGTGGCACCCTGGACTACCTG 216CATCTTCCAGGAGGACCACTCTCTGTGGCACCCTGGAC TACCTGCCCCCTGAAATGATTGAAGGTCGGAAURKB NM_004217 217 AGCTGCAGAAGAGCTGCACAT 218 GCATCTGCCAACTCCTCCAT 219TGACGAGCAGCGAACAGCCACG 220 AGCTGCAGAAGAGCTGCACATTTGACGAGCAGCGAACAGCCACGATCATGGAGGAGTTGGCAGATGC AXIN2 NM_004655 221 GGCTATGTCTTTGCACCAGC222 ATCCGTCAGCGCATCACT 223 ACCAGCGCCAACGACAGTGAGATA 224GGCTATGTCTTTGCACCAGCCACCAGCGCCAACGACAG TGAGATATCCAGTGATGCGCTGACGGATAZGP1 NM_001185 225 GAGGCCAGCTAGGAAGCAA 226 CAGGAAGGGCAGCTACTGG 227TCTGAGATCCCACATTGCCTCCAA 228 GAGGCCAGCTAGGAAGCAAGGGTTGGAGGCAATGTGGGATCTCAGACCCAGTAGCTGCCCTTCCTG BAD NM_032989 229 GGGTCAGGGGCCTCGAGAT 230CTGCTCACTCGGCTCAAACT 231 TGGGCCCAGAGCATGTTCCAGATC 232GGGTCAGGGGCCTCGAGATCGGGCTTGGGCCCAGAGCA CTGTTCCAGATCCCAGAGTTTGAGCCGAGTGAGCAG BAG5 NM_001015049 233ACTCCTGCAATGAACCCTGT 234 ACAAACAGCTCCCCACGA 235 ACACCGGATTTAGCTCTTGTCGGC236 ACTCCTGCAATGAACCCTGTTGACACCGGATTTAGCTC TTGTCGGCCTTCGTGGGGAGCTGTTTGTBAK1 NM_001188 237 CCATTCCCACCATTCTACCT 238 GGGAACATAGACCCACCAAT 239ACACCCCAGACGTCCTGGCCT 240 CCATTCCCACCATTCTACCTGAGGCCAGGACGTCTGGGGTGTGGGGATTGGTGGGTCTATGTTCCC BAX NM_004324 241 CCGCCGTGGACACAGACT 242TTGCCGTCAGAAAACATGTC 243 TGCCACTCGGAAAAAGACCTCTCG 244CCGCCGTGGACACAGACTCCCCCCGAGAGGTCTTTTTC A GCGAGTGGCAGCTGACATGTTTTCTGACGGCAA BBC3 NM_014417 245 CCTGGAGGGTCCTGTACAAT246 CTAATTGGGCTCCATCTCG 247 CATCATGGGACTCCTGCCCTTACC 248CCTGGAGGGTCCTGTACAATCTCATCATGGGACTCCTGCCCTTACCCAGGGGCCACAGAGCCCCCGAGATGGAGCC CAATTAG BCL2 NM_000633 249CAGATGGACCTAGTACCCACT 250 CCTATGATTTAAGGGCATTT 251TTCCACGCCGAAGGACAGCGAT 252 CAGATGGACCTAGTACCCACTGAGATTTCCACGCCGAA GAGATTCC GGACAGCGATGGGAAAAATGCCCTTAAATCATAGG BDKRB1 NM_000710 253GTGGCAGAAATCTACCTGGC 254 GAAGGGCAAGCCCAAGAC 255 ACCTGGCAGCCTCTGATCTGGTGT256 GTGGCAGAAATCTACCTGGCCAACCTGGCAGCCTCTGA TCTGGTGTTTGTCTTGGGCTTGCCCTTCBGN NM_001711 257 GAGCTCCGCAAGGATGAC 258 CTTGTTGTTCACCAGGACGA 259CAAGGGTCTCCAGCACCTCTACGC 260 GAGCTCCGCAAGGATGACTTCAAGGGTCTCCAGCACCTCTACGCCCTCGTCCTGGTGAACAACAAG BIK NM_001197 261 ATTCCTATGGCTCTGCAATTG 262GGCAGGAGTGAATGGCTCTT 263 CCGGTTAACTGTGGCCTGTGCCC 264ATTCCTATGGCTCTGCAATTGTCACCGGTTAACTGTGG TC CCCTGTGCCCAGGAAGAGCCATTCACTCCTGCC BIN1 NM_004305 265 CCTGCAAAAGGGAACAAGAG266 CGTGGTTGACTCTGATCTCG 267 CTTCGCCTCCAGATGGCTCCC 268CCTGCAAAAGGGAACAAGAGCCCTTCGCCTCCAGATGGCTCCCCTGCCGCCACCCCCGAGATCAGAGTCAACCACG BIRC5 NM_001012271 269TTCAGGTGGATGAGGAGACA 270 CACACAGCAGTGGCAAAAG 271TCTGCCAGACGCTTCCTATCACTC 272 TTCAGGTGGATGAGGAGACAGAATAGAGTGATAGGAAGTATTC CGTCTGGCAGATACTCCTTTTGCCACTGCTGTGTG BMP6 NM_001718 273GTGCAGACCTTGGTTCACCT 274 CTTAGTTGGCGCACAGCAC 275TGAACCCCGAGTATGTCCCCAAAC 276 GTGCAGACCTTGGTTCACCTTATGAACCCCGAGTATGTCCCCAAACCGTGCTGTGCGCCAACTAAG BMPR1B NM_001203 277 ACCACTTTGGCCATCCCT 278GCGGTGTTTGTACCCAGTG 279 ATTCACATTACCATAGCGGCCCCA 280ACCACTTTGGCCATCCCTGCATTTGGGGCCGCTATGGT AATGTGAATGCACTGGGTACAAACACCGCBRCA1 NM_007294 281 TCAGGGGGCTAGAAATCTGT 282 CCATTCCAGTTGATCTGTGG 283CTATGGGCCCTTCACCAACATGC 284 TCAGGGGGCTAGAAATCTGTTGCTATGGGCCCTTCACCAACATGCCCACAGATCAACTGGAATGG BRCA2 NM_000059 285 AGTTCGTGCTTTGCAAGATG 286AAGGTAAGCTGGGTCTGCTG 287 CATTCTTCACTGCTTCATAAAGCT 288AGTTCGTGCTTTGCAAGATGGTGCAGAGCTTTATGAAG CTGCACAGTGAAGAATGCAGCAGACCCAGCTTACCTT BTG1 NM_001731 289 GAGGTCCGAGCGATGTGA290 AGTTATTTTCGAGACAGGAG 291 CGCTCGTCTCTTCCTCTCTCCTGC 292GAGGTCCGAGCGATGTGACCAGGCCGCCATCGCTCGTC GCTCTTCCTCTCTCCTGCCGCCTCCTGTCTCGAAAATAAC T BTG3 NM_006806 293CCATATCGCCCAATTCCA 294 CCAGTGATTCCGGTCACAA 295 CATGGGTACCTCCTCCTGGAATGC296 CCATATCGCCCAATTCCAGTGACATGGGTACCTCCTCC TGGAATGCATTGTGACCGGAATCACTGGBTRC NM_033637 297 GTTGGGACACAGTTGGTCTG 298 TGAAGCAGTCAGTTGTGCTG 299CAGTCGGCCCAGGACGGTCTACT 300 GTTGGGACACAGTTGGTCTGCAGTCGGCCCAGGACGGTCTACTCAGCACAACTGACTGCTTCA BUB1 NM_004336 301 CCGAGGTTAATCCAGCACGTA 302AAGACATGGCGCTCTCAGTT 303 TGCTGGGAGCCTACACTTGGCCC 304CCGAGGTTAATCCAGCACGTATGGGGCCAAGTGTAGGC C TCCCAGCAGGAACTGAGAGCGCCATGTCTTC7 NM_000587 305 ATGTCTGAGTGTGAGGCGG 306 AGGCCTTATGCTGGTGACAG 307ATGCTCTGCCCTCTGCATCTCAGA 308 ATGTCTGAGTGTGAGGCGGGCGCTCTGAGATGCAGAGGGCAGAGCATCTCTGTCACCAGCATAAGGCCT CACNA1D NM_000720 309 AGGACCCAGCTCCATGTG310 CCTACATTCCGTGCCATTG 311 CAGTACACTGGCGTCCATTCCCTG 312AGGACCCAGCTCCATGTGCGTTCTCAGGGAATGGACGC CAGTGTACTGCCAATGGCACGGAATGTAGGCADM1 NM_014333 313 CCACCACCATCCTTACCATC 314 GATCCACTGCCCTGATCG 315TCTTCACCTGCTCGGGAATCTGTG 316 CCACCACCATCCTTACCATCATCACAGATTCCCGAGCAGGTGAAGAAGGCTCGATCAGGGCAGTGGATC CADPS NM_003716 317 CAGCAAGGAGACTGTGCTGA318 GGTCCTCTTCTCCACGGTAG 319 CTCCTGGATGGCCAAATTTGATGC 320CAGCAAGGAGACTGTGCTGAGCTCCTGGATGGCCAAAT AT TTGATGCCATCTACCGTGGAGAAGAGGACCCASP1 NM_001223 321 AACTGGAGCTGAGGTTGACA 322 CATCTACGCTGTACCCCAGA 323TCACAGGCATGACAATGCTGCTAC 324 AACTGGAGCTGAGGTTGACATCACAGGCATGACAATGC ATGCTACAAAATCTGGGGTACAGCGTAGATG CASP3 NM_032991 325 TGAGCCTGAGCAGAGACATGA326 CCTTCCTGCGTGGTCCAT 327 TCAGCCTGTTCCATGAAGGCAGAG 328TGAGCCTGAGCAGAGACATGACTCAGCCTGTTCCATGA C AGGCAGAGCCATGGACCACGCAGGAAGGCASP7 NM_033338 329 GCAGCGCCGAGACTTTTA 330 AGTCTCTCTCCGTCGCTCC 331CTTTCGCTAAAGGGGCCCCAGAC 332 GCAGCGCCGAGACTTTTAGTTTCGCTTTCGCTAAAGGGGCCCCAGACCCTTGCTGCGGAGCGACGGAGAGAGACT CAV1 NM_001753 333GTGGCTCAACATTGTGTTCC 334 CAATGGCCTCCATTTTACAG 335ATTTCAGCTGATCAGTGGGCCTCC 336 GTGGCTCAACATTGTGTTCCCATTTCAGCTGATCAGTGGGCCTCCAAGGAGGGGCTGTAAAATGGAGGCCATTG CAV2 NM_198212 337CTTCCCTGGGACGACTTG 338 CTCCTGGTCACCCTTCTGG 339 CCCGTACTGTCATGCCTCAGAGCT340 CTTCCCTGGGACGACTTGCCAGCTCTGAGGCATGACAG TACGGGCCCCCAGAAGGGTGACCAGGAGCCL2 NM_002982 341 CGCTCAGCCAGATGCAATC 342 GCACTGAGATCTTCCTATTG 343TGCCCCAGTCACCTGCTGTTA 344 CGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCT GTGAAGTTATAACTTCACCAATAGGAAGATCTCAGTGC CCL5 NM_002985 345AGGTTCTGAGCTCTGGCTTT 346 ATGCTGACTTCCTTCCTGGT 347 ACAGAGCCCTGGCAAAGCCAAG348 AGGTTCTGAGCTCTGGCTTTGCCTTGGCTTTGCCAGGG CTCTGTGACCAGGAAGGAAGTCAGCATCCNB1 NM_031966 349 TTCAGGTTGTTGCAGGAGAC 350 CATCTTCTTGGGCACACAAT 351TGTCTCCATTATTGATCGGTTCAT 352 TTCAGGTTGTTGCAGGAGACCATGTACATGACTGTCTC GCACATTATTGATCGGTTCATGCAGAATAATTGTGTGCCCA AGAAGATG CCND1 NM_001758 353GCATGTTCGTGGCCTCTAAGA 354 CGGTGTAGATGCACAGCTTC 355AAGGAGACCATCCCCCTGACGGC 356 GCATGTTCGTGGCCTCTAAGATGAAGGAGACCATCCCC TCCTGACGGCCGAGAAGCTGTGCATCTACACCG CCNE2 NM_057749 357ATGCTGTGGCTCCTTCCTAAC 358 ACCCAAATTGTGATATACAA 359TACCAAGCAACCTACATGTCAAGA 360 ATGCTGTGGCTCCTTCCTAACTGGGGCTTTCTTGACAT TAAAGGTT AAGCCC GTAGGTTGCTTGGTAATAACCTTTTTGTATATCACAAT TTGGGT CCNHNM_001239 361 GAGATCTTCGGTGGGGGTA 362 CTGCAGACGAGAACCCAAAC 363CATCAGCGTCCTGGCGTAAAACAC 364 GAGATCTTCGGTGGGGGTACGGGTGTTTTACGCCAGGACGCTGATGCGTTTGGGTTCTCGTCTGCAG CCR1 NM_001295 365 TCCAAGACCCAATGGGAA 366TCGTAGGCTTTCGTGAGGA 367 ACTCACCACACCTGCAGCCTTCAC 368TCCAAGACCCAATGGGAATTCACTCACCACACCTGCAG CCTTCACTTTCCTCACGAAAGCCTACGACD164 NM_006016 369 CAACCTGTGCGAAAGTCTACC 370 ACACCCAAGACCAGGACAAT 371CCTCCAATGAAACTGGCTGCATCA 372 CAACCTGTGCGAAAGTCTACCTTTGATGCAGCCAGTTTCATTGGAGGAATTGTCCTGGTCTTGGGTGT CD1A NM_001763 373 GGAGTGGAAGGAACTGGAAA374 TCATGGGCGTATCTACGAAT 375 CGCACCATTCGGTCATTTGAGG 376GGAGTGGAAGGAACTGGAAACATTATTCCGTATACGCACCATTCGGTCATTTGAGGGAATTCGTAGATACGCCCAT GA CD276 NM_001024736 377CCAAAGGATGCGATACACAG 378 GGATGACTTGGGAATCATGT 379CCACTGTGCAGCCTTATTTCTCCA 380 CCAAAGGATGCGATACACAGACCACTGTGCAGCCTTAT CATG TTCTCCAATGGACATGATTCCCAAGTCATCC CD44 NM_000610 381GGCACCACTGCTTATGAAGG 382 GATGCTCATGGTGAATGAGG 383ACTGGAACCCAGAAGCACACCCTC 384 GGCACCACTGCTTATGAAGGAAACTGGAACCCAGAAGCACACCCTCCCCTCATTCACCATGAGCATC CD68 NM_001251 385 TGGTTCCCAGCCCTGTGT 386CTCCTCCACCCTGGGTTGT 387 CTCCAAGCCCAGATTCAGATTCGA 388TGGTTCCCAGCCCTGTGTCCACCTCCAAGCCCAGATTC GTCAAGATTCGAGTCATGTACACAACCCAGGGTGGAGGAG CD82 NM_002231 389GTGCAGGCTCAGGTGAAGTG 390 GACCTCAGGGCGATTCATGA 391TCAGCTTCTACAACTGGACAGACA 392 GTGCAGGCTCAGGTGAAGTGCTGCGGCTGGGTCAGCTTACGCTG CTACAACTGGACAGACAACGCTGAGCTCATGAATCGCC CTGAGGTC CDC20 NM_001255393 TGGATTGGAGTTCTGGGAATG 394 GCTTGCACTCCACAGGTACA 395ACTGGCCGTGGCACTGGACAACA 396 TGGATTGGAGTTCTGGGAATGTACTGGCCGTGGCACTG CAGACAACAGTGTGTACCTGTGGAGTGCAAGC CDC25B NM_021873 397 GCTGCAGGACCAGTGAGG398 TAGGGCAGCTGGCTTCAG 399 CTGCTACCTCCCTTGCCTTTCGAG 400GCTGCAGGACCAGTGAGGGGCCTGCGCCAGTCCTGCTACCTCCCTTGCCTTTCGAGGCCTGAAGCCAGCTGCCCTA CDC6 NM_001254 401GCAACACTCCCCATTTACCTC 402 TGAGGGGGACCATTCTCTTT 403TTGTTCTCCACCAAAGCAAGGCAA 404 GCAACACTCCCCATTTACCTCCTTGTTCTCCACCAAAGCAAGGCAAGAAAGAGAATGGTCCCCCTCA CDH1 NM_004360 405 TGAGTGTCCCCCGGTATCTTC406 CAGCCGCTTTCAGATTTTCA 407 TGCCAATCCCGATGAAATTGGAAA 408TGAGTGTCCCCCGGTATCTTCCCCGCCCTGCCAATCCC T TTTGATGAAATTGGAAATTTTATTGATGAAAATCTGAAAGC GGCTG CDH10 NM_006727 409TGTGGTGCAAGTCACAGCTAC 410 TGTAAATGACTCTGGCGCTG 411ATGCCGATGACCCTTCATATGGGA 412 TGTGGTGCAAGTCACAGCTACAGATGCCGATGACCCTTCATATGGGAACAGCGCCAGAGTCATTTACA CDH11 NM_001797 413 GTCGGCAGAAGCAGGACT414 CTACTCATGGGCGGGATG 415 CCTTCTGCCCATAGTGATCAGCGA 416GTCGGCAGAAGCAGGACTTGTACCTTCTGCCCATAGTG ATCAGCGATGGCGGCATCCCGCCCATGAGTAGCDH19 NM_021153 417 AGTACCATAATGCGGGAACG 418 AGACTGCCTGTATAGGCTCC 419ACTCGGAAAACCACAAGCGCTGAG 420 AGTACCATAATGCGGGAACGCAAGACTCGGAAAACCAC TGAAGCGCTGAGATCAGGAGCCTATACAGGCAGTCT CDH5 NM_001795 421 ACAGGAGACGTGTTCGCC422 CAGCAGTGAGGTGGTACTCT 423 TATTCTCCCGGTCCAGCCTCTCAA 424ACAGGAGACGTGTTCGCCATTGAGAGGCTGGACCGGGA GA GAATATCTCAGAGTACCACCTCACTGCTGCDH7 NM_033646 425 GTTTGACATGGCTGCACTGA 426 AGTCACATCCCTCCGGGT 427ACCTCAACGTCATCCGAGACACCA 428 GTTTGACATGGCTGCACTGAGAAACCTCAACGTCATCCGAGACACCAAGACCCGGAGGGATGTGACT CDK14 NM_012395 429 GCAAGGTAAATGGGAAGTTGG430 GATAGCTGTGAAAGGTGTCC 431 CTTCCTGCAGCCTGATCACCTTCA 432GCAAGGTAAATGGGAAGTTGGTAGCTCTGAAGGTGATC CTAGGCTGCAGGAAGAAGAAGGGACACCTTTCACAGCTAT C CDK2 NM_001798 433AATGCTGCACTACGACCCTA 434 TTGGTCACATCCTGGAAGAA 435 CCTTGGCCGAAATCCGCTTGT436 AATGCTGCACTACGACCCTAACAAGCGGATTTCGGCCAAGGCAGCCCTGGCTCACCCTTTCTTCCAGGATGTGACC AA CDK3 NM_001258 437CCAGGAAGGGACTGGAAGA 438 GTTGCATGAGCAGGTCCC 439 CTCTGGCTCCAGATTGGGCACAAT440 CCAGGAAGGGACTGGAAGAGATTGTGCCCAATCTGGAG CCAGAGGGCAGGGACCTGCTCATGCAACCDK7 NM_001799 441 GTCTCGGGCAAAGCGTTAT 442 CTCTGGCCTTGTAAACGGTG 443CCTCCCCAAGGAAGTCCAGCTTCT 444 GTCTCGGGCAAAGCGTTATGAGAAGCTGGACTTCCTTGGGGAGGGACAGTTTGCCACCGTTTACAAGGCCAGAG CDKN1A NM_000389 445TGGAGACTCTCAGGGTCGAAA 446 GGCGTTTGGAGTGGTAGAAA 447 CGGCGGCAGACCAGCATGAC448 TGGAGACTCTCAGGGTCGAAAACGGCGGCAGACCAGCA TCTGACAGATTTCTACCACTCCAAACGCC CDKN1C NM_000076 449 CGGCGATCAAGAAGCTGT 450CAGGCGCTGATCTCTTGC 451 CGGGCCTCTGATCTCCGATTTCTT 452CGGCGATCAAGAAGCTGTCCGGGCCTCTGATCTCCGAT TTCTTCGCCAAGCGCAAGAGATCAGCGCCTGCDKN2B NM_004936 453 GACGCTGCAGAGCACCTT 454 GCGGGAATCTCTCCTCAGT 455CACAGGATGCTGGCCTTTGCTCTT 456 GACGCTGCAGAGCACCTTTGCACAGGATGCTGGCCTTTGCTCTTACTACACTGAGGAGAGATTCCCGC CDKN2C NM_001262 457 GAGCACTGGGCAATCGTTAC458 CAAAGGCGAACGGGAGTAG 459 CCTGTAACTTGAGGGCCACCGAAC 460GAGCACTGGGCAATCGTTACGACCTGTAACTTGAGGGC CACCGAACTGCTACTCCCGTTCGCCTTTGCDKN3 NM_005192 461 TGGATCTCTACCAGCAATGTG 462 ATGTCAGGAGTCCCTCCATC 463ATCACCCATCATCATCCAATCGCA 464 TGGATCTCTACCAGCAATGTGGAATTATCACCCATCATCATCCAATCGCAGATGGAGGGACTCCTGACAT CDS2 NM_003818 465 GGGCTTCTTTGCTACTGTGG466 ACAGGGCAGACAAAGCATCT 467 CCCGGACATCACATAGGACAGCAG 468GGGCTTCTTTGCTACTGTGGTGTTTGGCCTTCTGCTGTCCTATGTGATGTCCGGGTACAGATGCTTTGTCTGCCCT GT CENPF NM_016343 469CTCCCGTCAACAGCGTTC 470 GGGTGAGTCTGGCCTTCA 471 ACACTGGACCAGGAGTGCATCCAG472 CTCCCGTCAACAGCGTTCTTTCCAAACACTGGACCAGGAGTGCATCCAGATGAAGGCCAGACTCACCC CHAF1A NM_005483 473GAACTCAGTGTATGAGAAGCG 474 GCTCTGTAGCACCTGCGG 475TGCACGTACCAGCACATCCTGAAG 476 GAACTCAGTGTATGAGAAGCGGCCTGACTTCAGGATGT GGCTGGTACGTGCACCCGCAGGTGCTACAGAGC CHN1 NM_001822 477 TTACGACGCTCGTGAAAGC478 TCTCCCTGATGCACATGTCT 479 CCACCATTGGCCGCTTAGTGGTAT 480TTACGACGCTCGTGAAAGCACATACCACTAAGCGGCCA ATGGTGGTAGACATGTGCATCAGGGAGACHRAC1 NM_017444 481 TCTCGCTGCCTCTATCCC 482 CCTGGTTGATGCTGGACA 483ATCCGGGTCATCATGAAGAGCTCC 484 TCTCGCTGCCTCTATCCCGCATCCGGGTCATCATGAAGAGCTCCCCCGAGGTGTCCAGCATCAACCAGG CKS2 NM_001827 485 GGCTGGACGTGGTTTTGTCT486 CGCTGCAGAAAATGAAACGA 487 CTGCGCCCGCTCTTCGCG 488GGCTGGACGTGGTTTTGTCTGCTGCGCCCGCTCTTCGC GCTCTCGTTTCATTTTCTGCAGCG CLDN3NM_001306 489 ACCAACTGCGTGCAGGAC 490 GGCGAGAAGGAACAGCAC 491CAAGGCCAAGATCACCATCGTGG 492 ACCAACTGCGTGCAGGACGACACGGCCAAGGCCAAGATCACCATCGTGGCAGGCGTGCTGTTCCTTCTCGCC CLTC NM_004859 493ACCGTATGGACAGCCACAG 494 TGACTACAGGATCAGCGCTT 495TCTCACATGCTGTACCCAAAGCCA 496 ACCGTATGGACAGCCACAGCCTGGCTTTGGGTACAGCA CTGTGAGATGAAGCGCTGATCCTGTAGTCA COL11A1 NM_001854 497 GCCCAAGAGGGGAAGATG498 GGACCTGGGTCTCCAGTTG 499 CTGCTCGACCTTTGGGTCCTTCAG 500GCCCAAGAGGGGAAGATGGCCCTGAAGGACCCAAAGGT CGAGCAGGCCCAACTGGAGACCCAGGTCCCOL1A1 NM_000088 501 GTGGCCATCCAGCTGACC 502 CAGTGGTAGGTGATGTTCTG 503TCCTGCGCCTGATGTCCACCG 504 GTGGCCATCCAGCTGACCTTCCTGCGCCTGATGTCCAC GGACGAGGCCTCCCAGAACATCACCTACCACTG COL1A2 NM_000089 505CAGCCAAGAACTGGTATAGGA 506 AAACTGGCTGCCAGCATTG 507TCTCCTAGCCAGACGTGTTTCTTG 508 CAGCCAAGAACTGGTATAGGAGCTCCAAGGACAAGAAA GCTTCCTTG CACGTCTGGCTAGGAGAAACTATCAATGCTGGCAGCCA GTTT COL3A1 NM_000090 509GGAGGTTCTGGACCTGCTG 510 ACCAGGACTGCCACGTTC 511 CTCCTGGTCCCCAAGGTGTCAAAG512 GGAGGTTCTGGACCTGCTGGTCCTCCTGGTCCCCAAGG TGTCAAAGGTGAACGTGGCAGTCCTGGTCOL4A1 NM_001845 513 ACAAAGGCCTCCCAGGAT 514 GAGTCCCAGGAAGACCTGCT 515CTCCTTTGACACCAGGGATGCCAT 516 ACAAAGGCCTCCCAGGATTGGATGGCATCCCTGGTGTCAAAGGAGAAGCAGGTCTTCCTGGGACTC COL5A1 NM_000093 517 CTCCCTGGGAAAGATGGC 518CTGGACCAGGAAGCCCTC 519 CCAGGGAAACCACGTAATCCTGGA 520CTCCCTGGGAAAGATGGCCCTCCAGGATTACGTGGTTT CCCTGGGGACCGAGGGCTTCCTGGTCCAGCOL5A2 NM_000393 521 GGTCGAGGAACCCAAGGT 522 GCCTGGAGGTCCAACTCTG 523CCAGGAAATCCTGTAGCACCAGGC 524 GGTCGAGGAACCCAAGGTCCGCCTGGTGCTACAGGATTTCCTGGTTCTGCGGGCAGAGTTGGACCTCCAGGC COL6A1 NM_001848 525GGAGACCCTGGTGAAGCTG 526 TCTCCAGGGACACCAACG 527 CTTCTCTTCCCTGATCACCCTGCG528 GGAGACCCTGGTGAAGCTGGCCCGCAGGGTGATCAGGGAAGAGAAGGCCCCGTTGGTGTCCCTGGAGA COL6A3 NM_004369 529GAGAGCAAGCGAGACATTCTG 530 AACAGGGAACTGGCCCAC 531CCTCTTTGACGGCTCAGCCAATCT 532 GAGAGCAAGCGAGACATTCTGTTCCTCTTTGACGGCTCAGCCAATCTTGTGGGCCAGTTCCCTGTT COL8A1 NM_001850 533 TGGTGTTCCAGGGCTTCT 534CCCTGTAAACCCTGATCCC 535 CCTAAGGGAGAGCCAGGAATCCCA 536TGGTGTTCCAGGGCTTCTCGGACCTAAGGGAGAGCCAG GAATCCCAGGGGATCAGGGTTTACAGGGCOL9A2 NM_001852 537 GGGAACCATCCAGGGTCT 538 ATTCCGGGTGGACAGTTG 539ACACAGGAAATCCGCACTGCCTTC 540 GGGAACCATCCAGGGTCTGGAAGGCAGTGCGGATTTCCTGTGTCCAACCAACTGTCCACCCGGAAT CRISP3 NM_006061 541 TCCCTTATGAACAAGGAGCAC542 AACCATTGGTGCATAGTCCA 543 TGCCAGTTGCCCAGATAACTGTGA 544TCCCTTATGAACAAGGAGCACCTTGTGCCAGTTGCCCA TGATAACTGTGACGATGGACTATGCACCAATGGTT CSF1 NM_000757 545 TGCAGCGGCTGATTGACA546 CAACTGTTCCTGGTCTACAA 547 TCAGATGGAGACCTCGTGCCAAAT 548TGCAGCGGCTGATTGACAGTCAGATGGAGACCTCGTGC ACTCA TACACAAATTACATTTGAGTTTGTAGACCAGGAACAGTTG CSK NM_004383 549CCTGAACATGAAGGAGCTGA 550 CATCACGTCTCCGAACTCC 551 TCCCGATGGTCTGCAGCAGCT552 CCTGAACATGAAGGAGCTGAAGCTGCTGCAGACCATCG GGAAGGGGGAGTTCGGAGACGTGATGCSRP1 NM_004078 553 ACCCAAGACCCTGCCTCT 554 GCAGGGGTGGAGTGATGT 555CCACCCTTCTCCAGGGACCCTTAG 556 ACCCAAGACCCTGCCTCTTCCACTCCACCCTTCTCCAGGGACCCTTAGATCACATCACTCCACCCCTGC CTGF NM_001901 557 GAGTTCAAGTGCCCTGACG558 AGTTGTAATGGCAGGCACAG 559 AACATCATGTTCTTCTTCATGACC 560GAGTTCAAGTGCCCTGACGGCGAGGTCATGAAGAAGAA TCGCCATGATGTTCATCAAGACCTGTGCCTGCCATTACAACT CTHRC1 NM_138455 561TGGCTCACTTCGGCTAAAAT 562 TCAGCTCCATTGAATGTGAA 563CAACGCTGACAGCATGCATTTCTG 564 TGGCTCACTTCGGCTAAAATGCAGAAATGCATGCTGTC AAGCGTTGGTATTTCACATTCAATGGAGCTGA CTNNA1 NM_001903 565CGTTCCGATCCTCTATACTGC 566 AGGTCCCTGTTGGCCTTATA 567ATGCCTACAGCACCCTGATGTCGC 568 CGTTCCGATCCTCTATACTGCATCCCAGGCATGCCTAC ATGG A AGCACCCTGATGTCGCAGCCTATAAGGCCAACAGGGAC CT CTNNB1 NM_001904 569GGCTCTTGTGCGTACTGTCCT 570 TCAGATGACGAAGAGCACAG 571AGGCTCAGTGATGTCTTCCCTGTC 572 GGCTCTTGTGCGTACTGTCCTTCGGGCTGGTGACAGGG TATG ACCAG AAGACATCACTGAGCCTGCCATCTGTGCTCTTCGTCAT CTGA CTNND1 NM_001331573 CGGAAACTTCGGGAATGTGA 574 CTGAATCCTTCTGCCCAATC 575TTGATGCCCTCATTTTCATTGTTC 576 CGGAAACTTCGGGAATGTGATGGTTTAGTTGATGCCCT TCAGGC CATTTTCATTGTTCAGGCTGAGATTGGGCAGAAGGATT CAG CTNND2 NM_001332 577GCCCGTCCCTACAGTGAAC 578 CTCACACCCAGGAGTCGG 579 CTATGAAACGAGCCACTACCCGGC580 GCCCGTCCCTACAGTGAACTGAACTATGAAACGAGCCACTACCCGGCCTCCCCCGACTCCTGGGTGTGAG CTSB NM_001908 581 GGCCGAGATCTACAAAAACG582 GCAGGAAGTCCGAATACACA 583 CCCCGTGGAGGGAGCTTTCTC 584GGCCGAGATCTACAAAAACGGCCCCGTGGAGGGAGCTT TCTCTGTGTATTCGGACTTCCTGC CTSDNM_001909 585 GTACATGATCCCCTGTGAGAA 586 GGGACAGCTTGTAGCCTTTG 587ACCCTGCCCGCGATCACACTGA 588 GTACATGATCCCCTGTGAGAAGGTGTCCACCCTGCCCG GGT CCGATCACACTGAAGCTGGGAGGCAAAGGCTACAAGCTG TCCC CTSK NM_000396 589AGGCTTCTCTTGGTGTCCATA 590 CCACCTCTTCACTGGTCATG 591CCCCAGGTGGTTCATAGCCAGTTC 592 AGGCTTCTCTTGGTGTCCATACATATGAACTGGCTATG C TAACCACCTGGGGGACATGACCAGTGAAGAGGTGG CTSL2 NM_001333 593TGTCTCACTGAGCGAGCAGAA 594 ACCATTGCAGCCCTGATTG 595CTTGAGGACGCGAACAGTCCACCA 596 TGTCTCACTGAGCGAGCAGAATCTGGTGGACTGTTCGCGTCCTCAAGGCAATCAGGGCTGCAATGGT CTSS NM_004079 597 TGACAACGGCTTTCCAGTACA598 TCCATGGCTTTGTAGGGATA 599 TGATAACAAGGGCATCGACTCAGA 600TGACAACGGCTTTCCAGTACATCATTGATAACAAGGGC T GG CGCTATCGACTCAGACGCTTCCTATCCCTACAAAGCCATGGA CUL1 NM_003592 601ATGCCCTGGTAATGTCTGCAT 602 GCGACCACAAGCCTTATCAA 603CAGCCACAAAGCCAGCGTCATTGT 604 ATGCCCTGGTAATGTCTGCATTCAACAATGACGCTGGC GTTTGTGGCTGCTCTTGATAAGGCTTGTGGTCGC CXCL12 NM_000609 605GAGCTACAGATGCCCATGC 606 TTTGAGATGCTTGACGTTGG 607TTCTTCGAAAGCCATGTTGCCAGA 608 GAGCTACAGATGCCCATGCCGATTCTTCGAAAGCCATGTTGCCAGAGCCAACGTCAAGCATCTCAAA CXCR4 NM_003467 609 TGACCGCTTCTACCCCAATG610 AGGATAAGGCCAACCATGAT 611 CTGAAACTGGAACACAACCACCCA 612TGACCGCTTCTACCCCAATGACTTGTGGGTGGTTGTGT GT CAAGTCCAGTTTCAGCACATCATGGTTGGCCTTATCCT CXCR7 NM_020311 613CGCCTCAGAACGATGGAT 614 GTTGCATGGCCAGCTGAT 615 CTCAGAGCCAGGGAACTTCTCGGA616 CGCCTCAGAACGATGGATCTGCATCTCTTCGACTACTCAGAGCCAGGGAACTTCTCGGACATCAGCTGGCCATGCA AC CYP3A5 NM_000777 617TCATTGCCCAGTATGGAGATG 618 GACAGGCTTGCCTTTCTCTG 619TCCCGCCTCAAGTTTCTCACCAAT 620 TCATTGCCCAGTATGGAGATGTATTGGTGAGAAACTTGAGGCGGGAAGCAGAGAAAGGCAAGCCTGTC CYR61 NM_001554 621 TGCTCATTCTTGAGGAGCAT622 GTGGCTGCATTAGTGTCCAT 623 CAGCACCCTTGGCAGTTTCGAAAT 624TGCTCATTCTTGAGGAGCATTAAGGTATTTCGAAACTGCCAAGGGTGCTGGTGCGGATGGACACTAATGCAGCCAC DAG1 NM_004393 625GTGACTGGGCTCATGCCT 626 ATCCCACTTGTGCTCCTGTC 627 CAAGTCAGAGTTTCCCTGGTGCCC628 GTGACTGGGCTCATGCCTCCAAGTCAGAGTTTCCCTGG TGCCCCAGAGACAGGAGCACAAGTGGGATDAP NM_004394 629 CCAGCCTTTCTGGTGCTG 630 GACCAGGTCTGCCTCTGC 631CTCACCAGCTGGCAGACGTGAACT 632 CCAGCCTTTCTGGTGCTGTTCTCCAGTTCACGTCTGCCAGCTGGTGAGGGCAGAGGCAGACCTGGTC DAPK1 NM_004938 633 CGCTGACATCATGAATGTTCC634 TCTCTTTCAGCAACGATGTG 635 TCATATCCAAACTCGCCTCCAGCC 636CGCTGACATCATGAATGTTCCTCGACCGGCTGGAGGCG T TCTT GAGTTTGGATATGACAAAGACACATCGTTGCTGAAAGAG A DARC NM_002036 637GCCCTCATTAGTCCTTGGCT 638 CAGACAGAAGGGCTGGGAC 639TCAGCGCCTGTGCTTCCAAGATAA 640 GCCCTCATTAGTCCTTGGCTCTTATCTTGGAAGCACAGGCGCTGACAGCCGTCCCAGCCCTTCTGTCTG DDIT4 NM_019058 641 CCTGGCGTCTGTCCTCAC642 CGAAGAGGAGGTGGACGA 643 CTAGCCTTTGGGACCGCTTCTCGT 644CCTGGCGTCTGTCCTCACCATGCCTAGCCTTTGGGACC GCTTCTCGTCGTCGTCCACCTCCTCTTCGDDR2 NM_001014796 645 CTATTACCGGATCCAGGGC 646 CCCAGCAAGATACTCTCCCA 647AGTGCTCCCTATCCGCTGGATGTC 648 CTATTACCGGATCCAGGGCCGGGCAGTGCTCCCTATCCGCTGGATGTCTTGGGAGAGTATCTTGCTGGG DES NM_001927 649 ACTTCTCACTGGCCGACG 650GCTCCACCTTCTCGTTGGT 651 TGAACCAGGAGTTTCTGACCACGC 652ACTTCTCACTGGCCGACGCGGTGAACCAGGAGTTTCTG ACCACGCGCACCAACGAGAAGGTGGAGCDHRS9 NM_005771 653 GGAGAAAGGTCTCTGGGGTC 654 CAGTCAGTGGGAGCCAGC 655ATCAATAATGCTGGTGTTCCCGGC 656 GGAGAAAGGTCTCTGGGGTCTGATCAATAATGCTGGTGTTCCCGGCGTGCTGGCTCCCACTGACTG DHX9 NM_001357 657 GTTCGAACCATCTCAGCGAC 658TCCAGTTGGATTGTGGAGGT 659 CCAAGGAACCACACCCACTTGGTT 660GTTCGAACCATCTCAGCGACAAAACCAAGTGGGTGTGG TTCCTTGGTCACCTCCACAATCCAACTGGADIAPH1 NM_005219 661 CAAGCAGTCAAGGAGAACCA 662 AGTTTTGCTCGCCTCATCTT 663TTCTTCTGTCTCCCGCCGCTTC 664 CAAGCAGTCAAGGAGAACCAGAAGCGGCGGGAGACAGAAGAAAAGATGAGGCGAGCAAAACT DICER1 NM_177438 665 TCCAATTCCAGCATCACTGT 666GGCAGTGAAGGCGATAAAGT 667 AGAAAAGCTGTTTGTCTCCCCAGC 668TCCAATTCCAGCATCACTGTGGAGAAAAGCTGTTTGTC A TCCCCAGCATACTTTATCGCCTTCACTGCCDIO2 NM_013989 669 CTCCTTTCACGAGCCAGC 670 AGGAAGTCAGCCACTGAGGA 671ACTCTTCCACCAGTTTGCGGAAGG 672 CTCCTTTCACGAGCCAGCTGCCAGCCTTCCGCAAACTGGTGGAAGAGTTCTCCTCAGTGGCTGACTTCCT DLC1 NM_006094 673 GATTCAGACGAGGATGAGCC674 CACCTCTTGCTGTCCCTTTG 675 AAAGTCCATTTGCCACTGATGGCA 676GATTCAGACGAGGATGAGCCTTGTGCCATCAGTGGCAA ATGGACTTTCCAAAGGGACAGCAAGAGGTGDLGAP1 NM_004746 677 CTGCTGAGCCCAGTGGAG 678 AGCCTGGAAGGAGTTCCG 679CGCAGACCACCCATACTACACCCA 680 CTGCTGAGCCCAGTGGAGCACCACCCCGCAGACCACCCATACTACACCCAGCGGAACTCCTTCCAGGCT DLL4 NM_019074 681 CACGGAGGTATAAGGCAGGAG682 AGAAGGAAGGTCCAGCCG 683 CTACCTGGACATCCCTGCTCAGCC 684CACGGAGGTATAAGGCAGGAGCCTACCTGGACATCCCT GCTCAGCCCCGCGGCTGGACCTTCCTTCTDNM3 NM_015569 685 CTTTCCCACCCGGCTTAC 686 AAGGACCTTCTGCAGGTGTG 687CATATCGCTGACCGAATGGGAACC 688 CTTTCCCACCCGGCTTACAGACATATCGCTGACCGAATGGGAACCCCACACCTGCAGAAGGTCCTT DPP4 NM_001935 689 GTCCTGGGATCGGGAAGT 690GTACTCCCACCGGGATACAG 691 CGGCTATTCCACACTTGAACACGC 692GTCCTGGGATCGGGAAGTGGCGTGTTCAAGTGTGGAAT AGCCGTGGCGCCTGTATCCCGGTGGGAGTACDPT NM_001937 693 CACCTAGAAGCCTGCCCAC 694 CAGTAGCTCCCCAGGGTTC 695TTCCTAGGAAGGCTGGCAGACACC 696 CACCTAGAAGCCTGCCCACGATTCCTAGGAAGGCTGGCAGACACCCTGGAACCCTGGGGAGCTACTG DUSP1 NM_004417 697 AGACATCAGCTCCTGGTTCA698 GACAAACACCCTTCCTCCAG 699 CGAGGCCATTGACTTCATAGACTC 700AGACATCAGCTCCTGGTTCAACGAGGCCATTGACTTCA CATAGACTCCATCAAGAATGCTGGAGGAAGGGTGTTTGTC DUSP6 NM_001946 701CATGCAGGGACTGGGATT 702 TGCTCCTACCCTATCATTTG 703 TCTACCCTATGCGCCTGGAAGTCC704 CATGCAGGGACTGGGATTCGAGGACTTCCAGGCGCATA GGGGTAGAACCAAATGATAGGGTAGGAGCA DVL1 NM_004421 705 TCTGTCCCACCTGCTGCT 706TCAGACTGTTGCCGGATG 707 CTTGGAGCAGCCTGCACCTTCTCT 708TCTGTCCCACCTGCTGCTGCCCCTTGGAGCAGCCTGCA CCTTCTCTCCTCCCATCCGGCAACAGTCTGADYNLL1 NM_001037494 709 GCCGCCTACCTCACAGAC 710 GCCTGACTCCAGCTCTCCT 711ACCCACGTCAGTGAGTGCTCACAA 712 GCCGCCTACCTCACAGACTTGTGAGCACTCACTGACGTGGGTAGCGCCCAGGGCCTGCGGGGCGCAGGAGAGCTGG AGTCAGGC EBNA1BP2 NM_006824 713TGCGGCGAGATGGACACT 714 GTGACAAGGGATTCATCGGA 715 CCCGCTCTCGGATTCGGAGTCG716 TGCGGCGAGATGGACACTCCCCCGCTCTCGGATTCGGA TTGTCGGAATCCGATGAATCCCTTGTCAC ECE1 NM_001397 717 ACCTTGGGATCTGCCTCC 718GGACCAGGACCTCCATCTG 719 TCCACTCTCGATACCCTGCACCAG 720ACCTTGGGATCTGCCTCCAAGCTGGTGCAGGGTATCGA GAGTGGATTCCAGATGGAGGTCCTGGTCCEDN1 NM_001955 721 TGCCACCTGGACATCATTTG 722 TGGACCTAGGGCTTCCAAGT 723CACTCCCGAGCACGTTGTTCCGT 724 TGCCACCTGGACATCATTTGGGTCAACACTCCCGAGCA CCGTTGTTCCGTATGGACTTGGAAGCCCTAGGTCCA EDNRA NM_001957 725TTTCCTCAAATTTGCCTCAAG 726 TTACACATCCAACCAGTGCC 727CCTTTGCCTCAGGGCATCCTTTT 728 TTTCCTCAAATTTGCCTCAAGATGGAAACCCTTTGCCTCAGGGCATCCTTTTGGCTGGCACTGGTTGGATGTGTAA EFNB2 NM_004093 729TGACATTATCATCCCGCTAAG 730 GTAGTCCCCGCTGACCTTCT 731CGGACAGCGTCTTCTGCCCTCACT 732 TGACATTATCATCCCGCTAAGGACTGCGGACAGCGTCT GA CTCTGCCCTCACTACGAGAAGGTCAGCGGGGACTAC EGF NM_001963 733CTTTGCCTTGCTCTGTCACAG 734 AAATACCTGACACCCTTATG 735AGAGTTTAACAGCCCTGCTCTGGC 736 CTTTGCCTTGCTCTGTCACAGTGAAGTCAGCCAGAGCA TACAAATT TGACTT GGGCTGTTAAACTCTGTGAAATTTGTCATAAGGGTGTC AGGTATTT EGR1NM_001964 737 GTCCCCGCTGCAGATCTCT 738 CTCCAGCTTAGGGTAGTTGT 739CGGATCCTTTCCTCACTCGCCCA 740 GTCCCCGCTGCAGATCTCTGACCCGTTCGGATCCTTTC CCATCTCACTCGCCCACCATGGACAACTACCCTAAGCTGGAG EGR3 NM_004430 741CCATGTGGATGAATGAGGTG 742 TGCCTGAGAAGAGGTGAGGT 743ACCCAGTCTCACCTTCTCCCCACC 744 CCATGTGGATGAATGAGGTGTCTCCTTTCCATACCCAGTCTCACCTTCTCCCCACCCTACCTCACCTCTTCTCAGG CA EIF2C2 NM_012154 745GCACTGTGGGCAGATGAA 746 ATGTTTGGTGACTGGCGG 747 CGGGTCACATTGCAGACACGGTAC748 GCACTGTGGGCAGATGAAGAGGAAGTACCGCGTCTGCAATGTGACCCGGCGGCCCGCCAGTCACCAAACAT EIF2S3 NM_001415 749CTGCCTCCCTGATTCAAGTG 750 GGTGGCAAGTGCCTGTAATA 751TCTCGTGCTTCAGCCTCCCATGTA 752 CTGCCTCCCTGATTCAAGTGATTCTCGTGCTTCAGCCT TCCCCATGTAGCTGATATTACAGGCACTTGCCACC EIF3H NM_003756 753CTCATTGCAGGCCAGATAAA 754 GCCATGAAGAGCTTGCCTA 755CAGAACATCAAGGAGTTCACTGCC 756 CTCATTGCAGGCCAGATAAACACTTACTGCCAGAACAT CACAAGGAGTTCACTGCCCAAAACTTAGGCAAGCTCTTCA TGGC EIF4E NM_001968 757GATCTAAGATGGCGACTGTCG 758 TTAGATTCCGTTTTCTCCTC 759ACCACCCCTACTCCTAATCCCCCG 760 GATCTAAGATGGCGACTGTCGAACCGGAAACCACCCCT AATTCTG ACT ACTCCTAATCCCCCGACTACAGAAGAGGAGAAAACGGA ATCTAA EIF5 NM_001969761 GAATTGGTCTCCAGCTGCC 762 TCCAGGTATATGGCTCCTGC 763CCACTTGCACCCGAATCTTGATCA 764 GAATTGGTCTCCAGCTGCCTTTGATCAAGATTCGGGTGCAAGTGGAGCAGGAGCCATATACCTGGA ELK4 NM_001973 765 GATGTGGAGAATGGAGGGAA 766AGTCATTGCGGCTAGAGGTC 767 ATAAACCACCTCAGCCTGGTGCCA 768GATGTGGAGAATGGAGGGAAAGATAAACCACCTCAGCC TGGTGCCAAGACCTCTAGCCGCAATGACTENPP2 NM_006209 769 CTCCTGCGCACTAATACCTTC 770 TCCCTGGATAATTGGGTCTG 771TAACTTCCTCTGGCATGGTTGGCC 772 CTCCTGCGCACTAATACCTTCAGGCCAACCATGCCAGAGGAAGTTACCAGACCCAATTATCCAGGGA ENY2 NM_020189 773 CCTCAAAGAGTTGCTGAGAGC774 CCTCTTTACAGTGTGCCTTC 775 CTGATCCTTCCAGCCACATTCAAT 776CCTCAAAGAGTTGCTGAGAGCTAAATTAATTGAATGTG A TAATTTGCTGGAAGGATCAGTTGAAGGCACACTGTAAAGAGG EPHA2 NM_004431 777CGCCTGTTCACCAAGATTGAC 778 GTGGCGTGCCTCGAAGTC 779 TGCGCCCGATGAGATCACCG780 CGCCTGTTCACCAAGATTGACACCATTGCGCCCGATGAGATCACCGTCAGCAGCGACTTCGAGGCACGCCAC EPHA3 NM_005233 781CAGTAGCCTCAAGCCTGACA 782 TTCGTCCCATATCCAGCG 783 TATTCCAAATCCGAGCCCGAACAG784 CAGTAGCCTCAAGCCTGACACTATATACGTATTCCAAATCCGAGCCCGAACAGCCGCTGGATATGGGACGAA EPHB2 NM_004442 785CAACCAGGCAGCTCCATC 786 GTAATGCTGTCCACGGTGC 787 CACCTGATGCATGATGGACACTGC788 CAACCAGGCAGCTCCATCGGCAGTGTCCATCATGCATC AGGTGAGCCGCACCGTGGACAGCATTACEPHB4 NM_004444 789 TGAACGGGGTATCCTCCTTA 790 AGGTACCTCTCGGTCAGTGG 791CGTCCCATTTGAGCCTGTCAATGT 792 TGAACGGGGTATCCTCCTTAGCCACGGGGCCCGTCCCATTTGAGCCTGTCAATGTCACCACTGACCGAGAGGTACC T ERBB2 NM_004448 793CGGTGTGAGAAGTGCAGCAA 794 CCTCTCGCAAGTGCTCCAT 795CCAGACCATAGCACACTCGGGCAC 796 CGGTGTGAGAAGTGCAGCAAGCCCTGTGCCCGAGTGTGCTATGGTCTGGGCATGGAGCACTTGCGAGAGG ERBB3 NM_001982 797CGGTTATGTCATGCCAGATAC 798 GAACTGAGACCCACTGAAGA 799CCTCAAAGGTACTCCCTCCTCCCG 800 CGGTTATGTCATGCCAGATACACACCTCAAAGGTACTC ACAAGG G CCTCCTCCCGGGAAGGCACCCTTTCTTCAGTGGGTCTC AGTTC ERBB4 NM_005235 801TGGCTCTTAATCAGTTTCGTT 802 CAAGGCATATCGATCCTCAT 803TGTCCCACGAATAATGCGTAAATT 804 TGGCTCTTAATCAGTTTCGTTACCTGCCTCTGGAGAAT ACCTAAAGT CTCCAG TTACGCATTATTCGTGGGACAAAACTTTATGAGGATCG ATATGCCTTG ERCC1NM_001983 805 GTCCAGGTGGATGTGAAAGA 806 CGGCCAGGATACACATCTTA 807CAGCAGGCCCTCAAGGAGCTG 808 GTCCAGGTGGATGTGAAAGATCCCCAGCAGGCCCTCAAGGAGCTGGCTAAGATGTGTATCCTGGCCG EREG NM_001432 809 TGCTAGGGTAAACGAAGGCA810 TGGAGACAAGTCCTGGCAC 811 TAAGCCATGGCTGACCTCTGGAGC 812TGCTAGGGTAAACGAAGGCATAATAAGCCATGGCTGAC CTCTGGAGCACCAGGTGCCAGGACTTGTCTCCAERG NM_004449 813 CCAACACTAGGCTCCCCA 814 CCTCCGCCAGGTCTTTAGT 815AGCCATATGCCTTCTCATCTGGGC 816 CCAACACTAGGCTCCCCACCAGCCATATGCCTTCTCATCTGGGCACTTACTACTAAAGACCTGGCGGAGG ESR1 NM_000125 817 CGTGGTGCCCCTCTATGAC818 GGCTAGTGGGCGCATGTAG 819 CTGGAGATGCTGGACGCCC 820CGTGGTGCCCCTCTATGACCTGCTGCTGGAGATGCTGG ACGCCCACCGCCTACATGCGCCCACTAGCCESR2 NM_001437 821 TGGTCCATCGCCAGTTATCA 822 TGTTCTAGCGATCTTGCTTC 823ATCTGTATGCGGAACCTCAAAAGA 824 TGGTCCATCGCCAGTTATCACATCTGTATGCGGAACCT ACAGTCCCT CAAAAGAGTCCCTGGTGTGAAGCAAGATCGCTAGAACA ETV1 NM_004956 825TCAAACAAGAGCCAGGAATG 826 AACTGCCAGAGCTGAAGTGA 827ATCGGGAAGGACCCACATACCAAC 828 TCAAACAAGAGCCAGGAATGTATCGGGAAGGACCCACATACCAACGGCGAGGATCACTTCAGCTCTGGCAGTT ETV4 NM_001986 829TCCAGTGCCTATGACCCC 830 ACTGTCCAAGGGCACCAG 831 CAGACAAATCGCCATCAAGTCCCC832 TCCAGTGCCTATGACCCCCCCAGACAAATCGCCATCAA GTCCCCTGCCCCTGGTGCCCTTGGACAGTEZH2 NM_004456 833 TGGAAACAGCGAAGGATACA 834 CACCGAACACTCCCTAGTCC 835TCCTGACTTCTGTGAGCTCATTGC 836 TGGAAACAGCGAAGGATACAGCCTGTGCACATCCTGAC GTTCTGTGAGCTCATTGCGCGGGACTAGGGAGTGTTCGG TG F2R NM_001992 837AAGGAGCAAACCATCCAGG 838 GCAGGGTTTCATTGAGCAC 839 CCCGGGCTCAACATCACTACCTGT840 AAGGAGCAAACCATCCAGGTGCCCGGGCTCAACATCACTACCTGTCATGATGTGCTCAATGAAACCCTGC FAAH NM_001441 841 GACAGCGTAGTGGTGCATGT842 AGCTGAACATGGACTGTGGA 843 TGCCCTTCGTGCACACCAATG 844GACAGCGTAGTGGTGCATGTGCTGAAGCTGCAGGGTGCCGTGCCCTTCGTGCACACCAATGTTCCACAGTCCATGT TCAGCT FABP5 NM_001444 845GCTGATGGCAGAAAAACTCA 846 CTTTCCTTCCCATCCCACT 847CCTGATGCTGAACCAATGCACCAT 848 GCTGATGGCAGAAAAACTCAGACTGTCTGCAACTTTACAGATGGTGCATTGGTTCAGCATCAGGAGTGGGATGGGA AGGAAAG FADD NM_003824 849GTTTTCGCGAGATAACGGTC 850 CTCCGGTGCCTGATTCAC 851 AACGCGCTCTTGTCGATTTCCTGT852 GTTTTCGCGAGATAACGGTCGAAAACGCGCTCTTGTCG ATTTCCTGTAGTGAATCAGGCACCGGAGFAM107A NM_007177 853 AAGTCAGGGAAAACCTGCG 854 GCTGGCCCTACAGCTCTCT 855AATTGCCACACTGACCAGCGAAGA 856 AAGTCAGGGAAAACCTGCGGAGAATTGCCACACTGACCAGCGAAGAGAGAGAGCTGTAGGGCCAGC FAM13C NM_198215 857 ATCTTCAAAGCGGAGAGCG858 GCTGGATACCACATGCTCTG 859 TCCTGACTTTCTCCGTGGCTCCTC 860ATCTTCAAAGCGGAGAGCGGGAGGAGCCACGGAGAAAG TCAGGAGACAGAGCATGTGGTATCCAGCFAM171B NM_177454 861 CCAGGAAGGAAAAGCACTGT 862 GTGGTCTGCCCCTTCTTTTA 863TGAAGATTTTGAAGCTAATACATC 864 CCAGGAAGGAAAAGCACTGTTGAAGATTTTGAAGCTAACCCCAC TACATCCCCCACTAAAAGAAGGGGCAGACCAC FAM49B NM_016623 865AGATGCAGAAGGCATCTTGG 866 GCTGGATTGCCTCTCGTATT 867TGGCCAGCTCCTCTGTATGACTGC 868 AGATGCAGAAGGCATCTTGGAGGACTTGCAGTCATACAGAGGAGCTGGCCACGAAATACGAGAGGCAATCCAGC FAM73A NM_198549 869TGAGAAGGTGCGCTATTCAA 870 GGCCATTAAAAGCTCAGTGC 871AAGACCTCATGCAGTTACTCATTC 872 TGAGAAGGTGCGCTATTCAAGTACAGAGACTTTAGCTG GCCAAGACCTCATGCAGTTACTCATTCGCCGCACTGAGCTT TTAATGGCC FAP NM_004460 873GTTGGCTCACGTGGGTTAC 874 GACAGGACCGAAACATTCTG 875AGCCACTGCAAACATACTCGTTCA 876 GTTGGCTCACGTGGGTTACTGATGAACGAGTATGTTTG TCACAGTGGCTAAAAAGAGTCCAGAATGTTTCGGTCCTGTC FAS NM_000043 877GGATTGCTCAACAACCATGCT 878 GGCATTAACACTTTTGGACG 879TCTGGACCCTCCTACCTCTGGTTC 880 GGATTGCTCAACAACCATGCTGGGCATCTGGACCCTCC ATAATTACGT TACCTCTGGTTCTTACGTCTGTTGCTAGATTATCGTCC AAAAGTGTTAATGCC FASLGNM_000639 881 GCACTTTGGGATTCTTTCCAT 882 GCATGTAAGAAGACCCTCAC 883ACAACATTCTCGGTGCCTGTAACA 884 GCACTTTGGGATTCTTTCCATTATGATTCTTTGTTACA TATTGAA AAGAA GGCACCGAGAATGTTGTATTCAGTGAGGGTCTTCTTAC ATGC FASN NM_004104885 GCCTCTTCCTGTTCGACG 886 GCTTTGCCCGGTAGCTCT 887TCGCCCACCTACGTACTGGCCTAC 888 GCCTCTTCCTGTTCGACGGCTCGCCCACCTACGTACTGGCCTACACCCAGAGCTACCGGGCAAAGC FCGR3A NM_000569 889 GTCTCCAGTGGAAGGGAAAA890 AGGAATGCAGCTACTCACTG 891 CCCATGATCTTCAAGCAGGGAAGC 892GTCTCCAGTGGAAGGGAAAAGCCCATGATCTTCAAGCA G GGGAAGCCCCAGTGAGTAGCTGCATTCCTFGF10 NM_004465 893 TCTTCCGTCCCTGTCACCT 894 AGAGTTGGTGGCCTCTGGT 895ACACCATGTCCTGACCAAGGGCTT 896 TCTTCCGTCCCTGTCACCTGCCAAGCCCTTGGTCAGGACATGGTGTCACCAGAGGCCACCAACTCT FGF17 NM_003867 897 GGTGGCTGTCCTCAAAATCT898 TCTAGCCAGGAGGAGTTTGG 899 TTCTCGGATCTCCCTCAGTCTGCC 900GGTGGCTGTCCTCAAAATCTGCTTCTCGGATCTCCCTCAGTCTGCCCCCAGCCCCCAAACTCCTCCTGGCTAGA FGF5 NM_004464 901GCATCGGTTTCCATCTGC 902 AACATATTGGCTTCGTGGGA 903 CCATTGACTTTGCCATCCGGGTAG904 GCATCGGTTTCCATCTGCAGATCTACCCGGATGGCAAA GTCAATGGATCCCACGAAGCCAATATGTTFGF6 NM_020996 905 GGGCCATTAATTCTGACCAC 906 CCCGGGACATAGTGATGAA 907CATCCACCTTGCCTCTCAGGCAC 908 GGGCCATTAATTCTGACCACGTGCCTGAGAGGCAAGGTGGATGGCCCTGGGACAGAAACTGTTCATCACTATGTCC CGGG FGF7 NM_002009 909CCAGAGCAAATGGCTACAAA 910 TCCCCTCCTTCCATGTAATC 911CAGCCCTGAGCGACACACAAGAAG 912 CCAGAGCAAATGGCTACAAATGTGAACTGTTCCAGCCCTGAGCGACACACAAGAAGTTATGATTACATGGAAGGAG GGGA FGFR2 NM_000141 913GAGGGACTGTTGGCATGCA 914 GAGTGAGAATTCGATCCAAG 915TCCCAGAGACCAACGTTCAAGCAG 916 GAGGGACTGTTGGCATGCAGTGCCCTCCCAGAGACCAATCTTC TTG CGTTCAAGCAGTTGGTAGAAGACTTGGATCGAATTCTC ACTC FGFR4 NM_002011917 CTGGCTTAAGGATGGACAGG 918 ACGAGACTCCAGTGCTGATG 919CCTTTCATGGGGAGAACCGCATT 920 CTGGCTTAAGGATGGACAGGCCTTTCATGGGGAGAACCGCATTGGAGGCATTCGGCTGCGCCATCAGCACTGGAGT CTCGT FKBP5 NM_004117 921CCCACAGTAGAGGGGTCTCA 922 GGTTCTGGCTTTCACGTCTG 923TCTCCCCAGTTCCACAGCAGTGTC 924 CCCACAGTAGAGGGGTCTCATGTCTCCCCAGTTCCACAGCAGTGTCACAGACGTGAAAGCCAGAACC FLNA NM_001456 925 GAACCTGCGGTGGACACT 926GAAGACACCCTGGCCCTC 927 TACCAGGCCCATAGCACTGGACAC 928GAACCTGCGGTGGACACTTCCGGTGTCCAGTGCTATGG GCCTGGTATTGAGGGCCAGGGTGTCTTC FLNCNM_001458 929 CAGGACAATGGTGATGGCT 930 TGATGGTGTACTCGCCAGG 931ATGTGCTGTCAGCTACCTGCCCAC 932 CAGGACAATGGTGATGGCTCATGTGCTGTCAGCTACCTGCCCACGGAGCCTGGCGAGTACACCATCA FLT1 NM_002019 933 GGCTCCTGAATCTATCTTTG934 TCCCACAGCAATACTCCGTA 935 CTACAGCACCAAGAGCGACGTGTG 936GGCTCCTGAATCTATCTTTGACAAAATCTACAGCACCAAGAGCGACGTGTGGTCTTACGGAGTATTGCTGTGGGA FLT4 NM_002020 937ACCAAGAAGCTGAGGACCTG 938 CCTGGAAGCTGTAGCAGACA 939AGCCCGCTGACCATGGAAGATCT 940 ACCAAGAAGCTGAGGACCTGTGGCTGAGCCCGCTGACCATGGAAGATCTTGTCTGCTACAGCTTCCAGG FN1 NM_002026 941 GGAAGTGACAGACGTGAAGGT942 ACACGGTAGCCGGTCACT 943 ACTCTCAGGCGGTGTCCACATGAT 944GGAAGTGACAGACGTGAAGGTCACCATCATGTGGACAC CGCCTGAGAGTGCAGTGACCGGCTACCGTGTFOS NM_005252 945 CGAGCCCTTTGATGACTTCCT 946 GGAGCGGGCTGTCTCAGA 947TCCCAGCATCATCCAGGCCCAG 948 CGAGCCCTTTGATGACTTCCTGTTCCCAGCATCATCCAGGCCCAGTGGCTCTGAGACAGCCCGCTCC FOXO1 NM_002015 949 GTAAGCACCATGCCCCAC 950GGGGCAGAGGCACTTGTA 951 TATGAACCGCCTGACCCAAGTGAA 952GTAAGCACCATGCCCCACACCTCGGGTATGAACCGCCTGACCCAAGTGAAGACACCTGTACAAGTGCCTCTGCCCC FOXP3 NM_014009 953CTGTTTGCTGTCCGGAGG 954 GTGGAGGAACTCTGGGAATG 955 TGTTTCCATGGCTACCCCACAGGT956 CTGTTTGCTGTCCGGAGGCACCTGTGGGGTAGCCATGG AAACAGCACATTCCCAGAGTTCCTCCACFOXQ1 NM_033260 957 TGTTTTTGTCGCAACTTCCA 958 TGGAAAGGTTCCCTGATGTA 959TGATTTATGTCCCTTCCCTCCCCC 960 TGTTTTTGTCGCAACTTCCATTGATTTATGTCCCTTCC CTCTCCCCCCTAAGTACATCAGGGAACCTTTCCA FSD1 NM_024333 961 AGGCCTCCTGTCCTTCTACA962 TGTGTGAACCTGGTCTTGAA 963 CGCACCAAACAAGTGCTGCACA 964AGGCCTCCTGTCCTTCTACAATGCCCGCACCAAACAAG A TGCTGCACACTTTCAAGACCAGGTTCACACAFYN NM_002037 965 GAAGCGCAGATCATGAAGAA 966 CTCCTCAGACACCACTGCAT 967CTGAAGCACGACAAGCTGGTCCAG 968 GAAGCGCAGATCATGAAGAAGCTGAAGCACGACAAGCTGGTCCAGCTCTATGCAGTGGTGTCTGAGGAG G6PD NM_000402 969 AATCTGCCTGTGGCCTTG970 CGAGATGTTGCTGGTGACA 971 CCAGCCTCAGTGCCACTTGACATT 972AATCTGCCTGTGGCCTTGCCCGCCAGCCTCAGTGCCAC TTGACATTCCTTGTCACCAGCAACATCTCGGABRG2 NM_198904 973 CCACTGTCCTGACAATGACC 974 GAGATCCATCGCTGTGACAT 975CTCAGCACCATTGCCCGGAAAT 976 CCACTGTCCTGACAATGACCACCCTCAGCACCATTGCCCGGAAATCGCTCCCCAAGGTCTCCTATGTCACAGCGAT GGATCTC GADD45A NM_001924 977GTGCTGGTGACGAATCCA 978 CCCGGCAAAAACAAATAAGT 979 TTCATCTCAATGGAAGGATCCTGC980 GTGCTGGTGACGAATCCACATTCATCTCAATGGAAGGA CTCCTGCCTTAAGTCAACTTATTTGTTTTTGCCGGG GADD45B NM_015675 981ACCCTCGACAAGACCACACT 982 TGGGAGTTCATGGGTACAGA 983 TGGGAGTTCATGGGTACAGA984 ACCCTCGACAAGACCACACTTTGGGACTTGGGAGCTGGGGCTGAAGTTGCTCTGTACCCATGAACTCCCA GDF15 NM_004864 985CGCTCCAGACCTATGATGACT 986 ACAGTGGAAGGACCAGGACT 987TGTTAGCCAAAGACTGCCACTGCA 988 CGCTCCAGACCTATGATGACTTGTTAGCCAAAGACTGCCACTGCATATGAGCAGTCCTGGTCCTTCCACTGT GHR NM_000163 989 CCACCTCCCACAGGTTCA990 GGTGCGTGCCTGTAGTCC 991 CGTGCCTCAGCCTCCTGAGTAGCT 992CCACCTCCCACAGGTTCAGGCGATTCCCGTGCCTCAGC CTCCTGAGTAGCTGGGACTACAGGCACGCACCGNPTAB NM_024312 993 GGATTCACATCGCGGAAA 994 GTTCTTGCATAACAATCCGG 995CCCTGCTCACATGCCTCACATGAT 996 GGATTCACATCGCGGAAAGTCCCTGCTCACATGCCTCA TCCATGATTGACCGGATTGTTATGCAAGAAC GNRH1 NM_000825 997 AAGGGCTAAATCCAGGTGTG998 CTGGATCTCTGTGGCTGGT 999 TCCTGTCCTTCACTGTCCTTGCCA 1000AAGGGCTAAATCCAGGTGTGACGGTATCTAATGATGTCCTGTCCTTCACTGTCCTTGCCATCACCAGCCACAGAGA TCCAG GPM6B NM_001001994 1001ATGTGCTTGGAGTGGCCT 1002 TGTAGAACATAAACACGGGC 1003CGCTGAGAAACCAAACACACCCAG 1004 ATGTGCTTGGAGTGGCCTGGCTGGGTGTGTTTGGTTTC ATCAGCGGTGCCCGTGTTTATGTTCTACA GPNMB NM_001005340 1005 CAGCCTCGCCTTTAAGGAT1006 TGACAAATATGGCCAAGCAG 1007 CAAACAGTGCCCTGATCTCCGTTG 1008CAGCCTCGCCTTTAAGGATGGCAAACAGTGCCCTGATC TCCGTTGGCTGCTTGGCCATATTTGTCAGPR68 NM_003485 1009 CAAGGACCAGATCCAGCG 1010 GGTAGGGCAGGAAGCAGG 1011CTCAGCACCGTGGTCATCTTCCTG 1012 CAAGGACCAGATCCAGCGGCTGGTGCTCAGCACCGTGGTCATCTTCCTGGCCTGCTTCCTGCCCTACC GPS1 NM_004127 1013 AGTACAAGCAGGCTGCCAAG1014 GCAGCTCAGGGAAGTCACA 1015 CCTCCTGCTGGCTTCCTTTGATCA 1016AGTACAAGCAGGCTGCCAAGTGCCTCCTGCTGGCTTCC TTTGATCACTGTGACTTCCCTGAGCTGC GRB7NM_005310 1017 CCATCTGCATCCATCTTGTT 1018 GGCCACCAGGGTATTATCTG 1019CTCCCCACCCTTGAGAAGTGCCT 1020 CCATCTGCATCCATCTTGTTTGGGCTCCCCACCCTTGAGAAGTGCCTCAGATAATACCCTGGTGGCC GREM1 NM_013372 1021 GTGTGGGCAAGGACAAGC1022 GACCTGATTTGGCCTCACC 1023 TCCACCCTCCCTTTCTCACTCCAC 1024GTGTGGGCAAGGACAAGCAGGATAGTGGAGTGAGAAAG GGAGGGTGGAGGGTGAGGCCAAATCAGGTCGSK3B NM_002093 1025 GACAAGGACGGCAGCAAG 1026 TTGTGGCCTGTCTGGACC 1027CCAGGAGTTGCCACCACTGTTGTC 1028 GACAAGGACGGCAGCAAGGTGACAACAGTGGTGGCAACTCCTGGGCAGGGTCCAGACAGGCCACAA GSN NM_000177 1029 CTTCTGCTAAGCGGTACATCG1030 GGCTCAAAGCCTTGCTTCAC 1031 ACCCAGCCAATCGGGATCGGC 1032CTTCTGCTAAGCGGTACATCGAGACGGACCCAGCCAAT ACGGGATCGGCGGACGCCCATCACCGTGGTGAAGCAAGG CTTTGAGCC GSTM1 NM_000561 1033AAGCTATGAGGAAAAGAAGTA 1034 GGCCCAGCTTGAATTTTTCA 1035TCAGCCACTGGCTTCTGTCATAAT 1036 AAGCTATGAGGAAAAGAAGTACACGATGGGGGACGCTCCACGAT CAGGAG CTGATTATGACAGAAGCCAGTGGCTGAATGAAAAATTC AAGCTGGGCC GSTM2NM_000848 1037 CTGCAGGCACTCCCTGAAAT 1038 CCAAGAAACCATGGCTGCTT 1039CTGAAGCTCTACTCACAGTTTCTG 1040 CTGCAGGCACTCCCTGAAATGCTGAAGCTCTACTCACA GGGTTTCTGGGGAAGCAGCCATGGTTTCTTGG HDAC1 NM_004964 1041CAAGTACCACAGCGATGACTA 1042 GCTTGCTGTACTCCGACATG 1043TTCTTGCGCTCCATCCGTCCAGA 1044 CAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCATTAA TT CCATCCGTCCAGATAACATGTCGGAGTACAGCAAGC HDAC9 NM_178423 1045AACCAGGCAGTCACCTTGAG 1046 CTCTGTCTTCCTGCATCGC 1047CCCCCTGAAGCTCTTCCTCTGCTT 1048 AACCAGGCAGTCACCTTGAGGAAGCAGAGGAAGAGCTTCAGGGGGACCAGGCGATGCAGGAAGACAGAG HGD NM_000187 1049 CTCAGGTCTGCCCCTACAAT1050 TTATTGGTGCTCCGTGGAC 1051 CTGAGCAGCTCTCAGGATCGGCTT 1052CTCAGGTCTGCCCCTACAATCTCTATGCTGAGCAGCTCTCAGGATCGGCTTTCACTTGTCCACGGAGCACCAATAA HIP1 NM_005338 1053CTCAGAGCCCCACCTGAG 1054 GGGTTTCCCTGCCATACTG 1055CGACTCACTGACCGAGGCCTGTAA 1056 CTCAGAGCCCCACCTGAGCCTGCCGACTCACTGACCGAGGCCTGTAAGCAGTATGGCAGGGAAACCC HIRIP3 NM_003609 1057 GGATGAGGAAAAGGGGGAT1058 TCCCTAGCTGACTTTCTCCG 1059 CCATTGCTCCTGGTTCTGGGTTTC 1060GGATGAGGAAAAGGGGGATTGGAAACCCAGAACCAGGA GCAATGGCCGGAGAAAGTCAGCTAGGGA HK1NM_000188 1061 TACGCACAGAGGCAAGCA 1062 GAGAGAAGTGCTGGAGAGGC 1063TAAGAGTCCGGGATCCCCAGCCTA 1064 TACGCACAGAGGCAAGCAGCTAAGAGTCCGGGATCCCCAGCCTACTGCCTCTCCAGCACTTCTCTC HLA-G NM_002127 1065 CCATCCCCATCATGGGTATC1066 CCGCAGCTCCAGTGACTACA 1067 CTGCAAGGACAACCAGGCCAGCAA 1068CCTGCGCGGCTACTACAACCAGAGCGAGGCCAGTTCTC ACACCCTCCAGTGGATGATTGGCTGCGACCTGHLF NM_002126 1069 CACCCTGCAGGTGTCTGAG 1070 GGTACCTAGGAGCAGAAGGT 1071TAAGTGATCTGCCCTCCAGGTGGC 1072 CACCCTGCAGGTGTCTGAGACTAAGTGATCTGCCCTCC GAAGGTGGCGATCACCTTCTGCTCCTAGGTACC HNF1B NM_000458 1073 TCCCAGCATCTCAACAAGG1074 CGTACCAGGTGTACAGAGCG 1075 CCCCTATGAAGACCCAGAAGCGTG 1076TCCCAGCATCTCAACAAGGGCACCCCTATGAAGACCCA GAAGCGTGCCGCTCTGTACACCTGGTACGHPS1 NM_000195 1077 GCGGAAGCTGTATGTGCTC 1078 TTCGGATAAGATGACCGTCC 1079CAGTCACCAGCCCAAAGTGCACTT 1080 GCGGAAGCTGTATGTGCTCAAGTACCTGTTTGAAGTGCACTTTGGGCTGGTGACTGTGGACGGTCATCTTATCCGA A HRAS NM_005343 1081GGACGAATACGACCCCACT 1082 GCACGTCTCCCCATCAAT 1083ACCACCTGCTTCCGGTAGGAATCC 1084 GGACGAATACGACCCCACTATAGAGGATTCCTACCGGAAGCAGGTGGTCATTGATGGGGAGACGTGC HSD17B10 NM_004493 1085CCAGCGAGTTCTTGATGTGA 1086 ATCTCACCAGCCACCAGG 1087TCATGGGCACCTTCAATGTGATCC 1088 CCACCAGACAAGACCGATTCGCTGGCCTCCATTTCTTCAACCCAGTGCCTGTCATGAAACTTGTGG HSD17B2 NM_002153 1089 GCTTTCCAAGTGGGGAATTA1090 TGCCTGCGATATTTGTTAGG 1091 AGTTGCTTCCATCCAACCTGGAGG 1092GCTTTCCAAGTGGGGAATTAAAGTTGCTTCCATCCAAC CTGGAGGCTTCCTAACAAATATCGCAGGCAHSD17B3 NM_000197 1093 GGGACGTCCTGGAACAGT 1094 TGGAGAATCTCACGCACTTC 1095CTTCATCCTCACAGGGCTGCTGGT 1096 GGGACGTCCTGGAACAGTTCTTCATCCTCACAGGGCTGCTGGTGTGCCTGGCCTGCCTGGCGAAGTGCGTGAGATT CTCCA HSD17B4 NM_000414 1097CGGGAAGCTTCAGAGTACCTT 1098 ACCTCAGGCCCAATATCCTT 1099AGGCGGCGTCCTATTTCCTCAAAT 1100 CGGGAAGCTTCAGAGTACCTTTGTATTTGAGGAAATAGGACGCCGCCTAAAGGATATTGGGCCTGAGGT HSD3B2 NM_000198 1101GCCTTCCTTTAACCCTGATG 1102 GGAGTAAATTGGGCTGAGTA 1103ACTTCCAGCAGGAAGCCAATCCAG 1104 GCCTTCCTTTAACCCTGATGTACTGGATTGGCTTCCTG GGCTGGAAGTAGTGAGCTTCCTACTCAGCCCAATTTACTC C HSP90AB1 NM_007355 1105GCATTGTGACCAGCACCTAC 1106 GAAGTGCCTGGGCTTTCAT 1107ATCCGCTCCATATTGGCTGTCCAG 1108 GCATTGTGACCAGCACCTACGGCTGGACAGCCAATATGGAGCGGATCATGAAAGCCCAGGCACTTC HSPA5 NM_005347 1109 GGCTAGTAGAACTGGATCCCA1110 GGTCTGCCCAAATGCTTTTC 1111 TAATTAGACCTAGGCCTCAGCTGC 1112GGCTAGTAGAACTGGATCCCAACACCAAACTCTTAATT ACA ACTGCCAGACCTAGGCCTCAGCTGCACTGCCCGAAAAGCATTTG GGCAGACC HSPA8 NM_006597 1113CCTCCCTCTGGTGGTGCTT 1114 GCTACATCTACACTTGGTTG 1115CTCAGGGCCCACCATTGAAGAGGT 1116 CCTCCCTCTGGTGGTGCTTCCTCAGGGCCCACCATTGAGCTTAA TG AGAGGTTGATTAAGCCAACCAAGTGTAGATGTAGC HSPB1 NM_001540 1117CCGACTGGAGGAGCATAAA 1118 ATGCTGGCTGACTCTGCTC 1119CGCACTTTTCTGAGCAGACGTCCA 1120 CCGACTGGAGGAGCATAAAAGCGCAGCCGAGCCCAGCGCCCCGCACTTTTCTGAGCAGACGTCCAGAGCAGAGTCA GCCAGCAT HSPB2 NM_001541 1121CACCACTCCAGAGGTAGCAG 1122 TGGGACCAAACCATACATTG 1123CACCTTTCCCTTCCCCCAAGGAT 1124 CACCACTCCAGAGGTAGCAGCATCCTTGGGGGAAGGGAAAGGTGCATGGTCCACAATGTATGGTTTGGTCCCA HSPE1 NM_002157 1125GCAAGCAACAGTAGTCGCTG 1126 CCAACTTTCACGCTAACTGG 1127TCTCCACCCTTTCCTTTAGAACCC 1128 GCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTAAAG T GGAAAGGGTGGAGAGATTCAACCAGTTAGCGTGAAAGTT GG HSPG2 NM_005529 1129GAGTACGTGTGCCGAGTGTT 1130 CTCAATGGTGACCAGGACA 1131CAGCTCCGTGCCTCTAGAGGCCT 1132 GAGTACGTGTGCCGAGTGTTGGGCAGCTCCGTGCCTCTAGAGGCCTCTGTCCTGGTCACCATTGAG ICAM1 NM_000201 1133 GCAGACAGTGACCATCTACAG1134 CTTCTGAGACCTCTGGCTTC 1135 CCGGCGCCCAACGTGATTCT 1136GCAGACAGTGACCATCTACAGCTTTCCGGCGCCCAACG CTT GTTGATTCTGACGAAGCCAGAGGTCTCAGAAG IER3 NM_003897 1137 GTACCTGGTGCGCGAGAG1138 GCGTCTCCGCTGTAGTGTT 1139 TCAAGTTGCCTCGGAAGTCCCAGT 1140GTACCTGGTGCGCGAGAGCGTATCCCCAACTGGGACTTCCGAGGCAACTTGAACTCAGAACACTACAGCGGAGACG C IFI30 NM_006332 1141ATCCCATGAAGCCCAGATAC 1142 GCACCATTCTTAGTGGAGCA 1143AAAATTCCACCCCATGATCAAGAA 1144 ATCCCATGAAGCCCAGATACACAAAATTCCACCCCATG TCCATCAAGAATCCTGCTCCACTAAGAATGGTGC IFIT1 NM_001548 1145TGACAACCAAGCAAATGTGA 1146 CAGTCTGCCCATGTGGTAAT 1147AAGTTGCCCCAGGTCACCAGACTC 1148 TGACAACCAAGCAAATGTGAGGAGTCTGGTGACCTGGGCGCAATTTGCCTGGATGTATTACCACATGGGCAGACTG IFNG NM_000619 1149GCTAAAACAGGGAAGCGAAA 1150 CAACCATTACTGGGATGCTC 1151TCGACCTCGAAACAGCATCTGACT 1152 GCTAAAACAGGGAAGCGAAAAAGGAGTCAGATGCTGTT CCTCGAGGTCGAAGAGCATCCCAGTAATGGTTG IGF1 NM_000618 1153TCCGGAGCTGTGATCTAAGGA 1154 CGGACAGAGCGAGCTGACTT 1155TGTATTGCGCACCCCTCAAGCCTG 1156 TCCGGAGCTGTGATCTAAGGAGGCTGGAGATGTATTGCGCACCCCTCAAGCCTGCCAAGTCAGCTCGCTCTGTCCG IGF1R NM_000875 1157GCATGGTAGCCGAAGATTTCA 1158 TTTCCGGTAATAGTCTGTCT 1159CGCGTCATACCAAAATCTCCGATT 1160 GCATGGTAGCCGAAGATTTCACAGTCAAAATCGGAGATCATAGATATC TTGA TTTGGTATGACGCGAGATATCTATGAGACAGACTATTA CCGGAAA IGF2NM_000612 1161 CCGTGCTTCCGGACAACTT 1162 TGGACTGCTTCCAGGTGTCA 1163TACCCCGTGGGCAAGTTCTTCCAA 1164 CCGTGCTTCCGGACAACTTCCCCAGATACCCCGTGGGCAAGTTCTTCCAATATGACACCTGGAAGCAGTCCA IGFBP2 NM_000597 1165GTGGACAGCACCATGAACA 1166 CCTTCATACCCGACTTGAGG 1167 CTTCCGGCCAGCACTGCCTC1168 GTGGACAGCACCATGAACATGTTGGGCGGGGGAGGCAGTGCTGGCCGGAAGCCCCTCAAGTCGGGTATGAAGG IGFBP3 NM_000598 1169ACATCCCAACGCATGCTC 1170 CCACGCCCTTGTTTCAGA 1171 ACACCACAGAAGGCTGTGAGCTCC1172 ACATCCCAACGCATGCTCCTGGAGCTCACAGCCTTCTG TGGTGTCATTTCTGAAACAAGGGCGTGGIGFBP5 NM_000599 1173 TGGACAAGTACGGGATGAAGC 1174 CGAAGGTGTGGCACTGAAAG1175 CCCGTCAACGTACTCCATGCCTGG 1176TGGACAAGTACGGGATGAAGCTGCCAGGCATGGAGTAC T TGTTGACGGGGACTTTCAGTGCCACACCTTCG IGFBP6 NM_002178 1177TGAACCGCAGAGACCAACAG 1178 GTCTTGGACACCCGCAGAAT 1179ATCCAGGCACCTCTACCACGCCCT 1180 TGAACCGCAGAGACCAACAGAGGAATCCAGGCACCTCT CACCACGCCCTCCCAGCCCAATTCTGCGGGTGTCCAAGA C IL10 NM_000572 1181CTGACCACGCTTTCTAGCTG 1182 CCAAGCCCAGAGACAAGATA 1183TTGAGCTGTTTTCCCTGACCTCCC 1184 CTGACCACGCTTTCTAGCTGTTGAGCTGTTTTCCCTGA ACCTCCCTCTAATTTATCTTGTCTCTGGGCTTGG IL11 NM_000641 1185TGGAAGGTTCCACAAGTCAC 1186 TCTTGACCTTGCAGCTTTGT 1187CCTGTGATCAACAGTACCCGTATG 1188 TGGAAGGTTCCACAAGTCACCCTGTGATCAACAGTACC GGCGTATGGGACAAAGCTGCAAGGTCAAGA IL17A NM_002190 1189 TCAAGCAACACTCCTAGGGC1190 CAGCTCCTTTCTGGGTTGTG 1191 TGGCTTCTGTCTGATCAAGGCACC 1192TCAAGCAACACTCCTAGGGCCTGGCTTCTGTCTGATCA AGGCACCACACAACCCAGAAAGGAGCTG IL1ANM_000575 1193 GGTCCTTGGTAGAGGGCTACT 1194 GGATGGAGCTTCAGGAGAGA 1195TCTCCACCCTGGCCCTGTTACAGT 1196 GGTCCTTGGTAGAGGGCTACTTTACTGTAACAGGGCCA TGGGTGGAGAGTTCTCTCCTGAAGCTCCATCC IL1B NM_000576 1197 AGCTGAGGAAGATGCTGGTT1198 GGAAAGAAGGTGCTCAGGTC 1199 TGCCCACAGACCTTCCAGGAGAAT 1200AGCTGAGGAAGATGCTGGTTCCCTGCCCACAGACCTTC CAGGAGAATGACCTGAGCACCTTCTTTCC IL2NM_000586 1201 ACCTCAACTCCTGCCACAAT 1202 CACTGTTTGTGACAAGTGCA 1203TGCAACTCCTGTCTTGCATTGCAC 1204 ACCTCAACTCCTGCCACAATGTACAGGATGCAACTCCT AGGTCTTGCATTGCACTAAGTCTTGCACTTGTCACAAACA GTG IL6 NM_000600 1205CCTGAACCTTCCAAAGATGG 1206 ACCAGGCAAGTCTCCTCATT 1207CCAGATTGGAAGCATCCATCTTTT 1208 CCTGAACCTTCCAAAGATGGCTGAAAAAGATGGATGCT TCATCCAATCTGGATTCAATGAGGAGACTTGCCTGGT IL6R NM_000565 1209CCAGCTTATCTCAGGGGTGT 1210 CTGGCGTAGAACCTTCCG 1211CCTTTGGCTTCACGGAAGAGCCTT 1212 CCAGCTTATCTCAGGGGTGTGCGGCCTTTGGCTTCACGGAAGAGCCTTGCGGAAGGTTCTACGCCAG IL6ST NM_002184 1213 GGCCTAATGTTCCAGATCCT1214 AAAATTGTGCCTTGGAGGAG 1215 CATATTGCCCAGTGGTCACCTCAC 1216GGCCTAATGTTCCAGATCCTTCAAAGAGTCATATTGCC ACAGTGGTCACCTCACACTCCTCCAAGGCACAATTTT IL8 NM_000584 1217AAGGAACCATCTCACTGTGTG 1218 ATCAGGAAGGCTGCCAAGAG 1219TGACTTCCAAGCTGGCCGTGGC 1220 AAGGAACCATCTCACTGTGTGTAAACATGACTTCCAAG TAAACCTGGCCGTGGCTCTCTTGGCAGCCTTCCTGAT ILF3 NM_004516 1221 GACACGCCAAGTGGTTCC1222 CTCAAGACCCGGATCACAA 1223 ACACAAGACTTCAGCCCGTTGGCT 1224GACACGCCAAGTGGTTCCAGGCCAGAGCCAACGGGCTG AAGTCTTGTGTCATTGTGATCCGGGTCTTGAGILK NM_001014794 1225 CTCAGGATTTTCTCGCATCC 1226 AGGAGCAGGTGGAGACTGG 1227ATGTGCTCCCAGTGCTAGGTGCCT 1228 CTCAGGATTTTCTCGCATCCAAATGTGCTCCCAGTGCTAGGTGCCTGCCAGTCTCCACCTGCTCCT IMMT NM_006839 1229 CTGCCTATGCCAGACTCAGA1230 GCTTTTCTGGCTTCCTCTTC 1231 CAACTGCATGGCTCTGAACAGCCT 1232CTGCCTATGCCAGACTCAGAGGAATCGAACAGGCTGTTCAGAGCCATGCAGTTGCTGAAGAGGAAGCCAGAAAAGC ING5 NM_032329 1233CCTACAGCAAGTGCAAGGAA 1234 CATCTCGTAGGTCTGCATGG 1235CCAGCTGCACTTTGTCGTCACTGT 1236 CCTACAGCAAGTGCAAGGAATACAGTGACGACAAAGTGCAGCTGGCCATGCAGACCTACGAGATG INHBA NM_002192 1237 GTGCCCGAGCCATATAGCA1238 CGGTAGTGGTTGATGACTGT 1239 ACGTCCGGGTCCTCACTGTCCTTC 1240GTGCCCGAGCCATATAGCAGGCACGTCCGGGTCCTCAC TGA CTGTCCTTCCACTCAACAGTCATCAACCACTACCG INSL4 NM_002195 1241CTGTCATATTGCCCCATGC 1242 CAGATTCCAGCAGCCACC 1243TGAGAAGACATTCACCACCACCCC 1244 CTGTCATATTGCCCCATGCCTGAGAAGACATTCACCACCACCCCAGGAGGGTGGCTGCTGGAATCTG ITGA1 NM_181501 1245 GCTTCTTCTGGAGATGTGCTC1246 CCTGTAGATAATGACCTGGC 1247 TTGCTGGACAGCCTCGGTACAATC 1248GCTTCTTCTGGAGATGTGCTCTATATTGCTGGACAGCC T CTTCGGTACAATCATACAGGCCAGGTCATTATCTACAGG ITGA3 NM_002204 1249CCATGATCCTCACTCTGCTG 1250 GAAGCTTTGTAGCCGGTGAT 1251CACTCCAGACCTCGCTTAGCATGG 1252 CCATGATCCTCACTCTGCTGGTGGACTATACACTCCAGACCTCGCTTAGCATGGTAAATCACCGGCTACAAAGCTT C ITGA4 NM_000885 1253CAACGCTTCAGTGATCAATCC 1254 GTCTGGCCGGGATTCTTT 1255CGATCCTGCATCTGTAAATCGCCC 1256 CAACGCTTCAGTGATCAATCCCGGGGCGATTTACAGATGCAGGATCGGAAAGAATCCCGGCCAGAC ITGA5 NM_002205 1257 AGGCCAGCCCTACATTATCA1258 GTCTTCTCCACAGTCCAGCA 1259 TCTGAGCCTTGTCCTCTATCCGGC 1260AGGCCAGCCCTACATTATCAGAGCAAGAGCCGGATAGAGGACAAGGCTCAGATCTTGCTGGACTGTGGAGAAGAC ITGA6 NM_000210 1261CAGTGACAAACAGCCCTTCC 1262 GTTTAGCCTCATGGGCGTC 1263TCGCCATCTTTTGTGGGATTCCTT 1264 CAGTGACAAACAGCCCTTCCAACCCAAGGAATCCCACAAAAGATGGCGATGACGCCCATGAGGCTAAAC ITGA7 NM_002206 1265GATATGATTGGTCGCTGCTTT 1266 AGAACTTCCATTCCCCACCA 1267CAGCCAGGACCTGGCCATCCG 1268 GATATGATTGGTCGCTGCTTTGTGCTCAGCCAGGACCT G TGGCCATCCGGGATGAGTTGGATGGTGGGGAATGGAAGT TCT ITGAD NM_005353 1269GAGCCTGGTGGATCCCAT 1270 ACTGTCAGGATGCCCGTG 1271 CAACTGAAAGGCCTGACGTTCACG1272 GAGCCTGGTGGATCCCATCGTCCAACTGAAAGGCCTGA CGTTCACGGCCACGGGCATCCTGACAGTITGB3 NM_000212 1273 ACCGGGAGCCCTACATGAC 1274 CCTTAAGCTCTTTCACTGAC 1275AAATACCTGCAACCGTTACTGCCG 1276 ACCGGGGAGCCCTACATGACGAAAATACCTGCAACCGTTCAATCT TGAC TACTGCCGTGACGAGATTGAGTCAGTGAAAGAGCTTAA GG ITGB4 NM_0002131277 CAAGGTGCCCTCAGTGGA 1278 GCGCACACCTTCATCTCAT 1279CACCAACCTGTACCCGTATTGCGA 1280 CAAGGTGCCCTCAGTGGAGCTCACCAACCTGTACCCGTATTGCGACTATGAGATGAAGGTGTGCGC ITGB5 NM_002213 1281 TCGTGAAAGATGACCAGGAG1282 GGTGAACATCATGACGCAGT 1283 TGCTATGTTTCTACAAAACCGCCA 1284TCGTGAAAGATGACCAGGAGGCTGTGCTATGTTTCTAC AGGAAAACCGCCAAGGACTGCGTCATGATGTTCACC ITPR1 NM_002222 1285GAGGAGGTGTGGGTGTTCC 1286 GTAATCCCATGTCCGCGA 1287CCATCCTAACGGAACGAGCTCCCT 1288 GAGGAGGTGTGGGTGTTCCGCTTCCATCCTAACGGAACGAGCTCCCTCTTCGCGGACATGGGATTAC ITPR3 NM_002224 1289 TTGCCATCGTGTCAGTGC1290 ATGGAGCTGGCGTCATTG 1291 TCCAGGTCTCGGATCTCAGACACG 1292TTGCCATCGTGTCAGTGCCCGTGTCTGAGATCCGAGAC CTGGACTTTGCCAATGACGCCAGCTCCATITSN1 NM_003024 1293 TAACTGGGATGCATGGGC 1294 CTCTGCCTTAACTGGCCG 1295AGCCCTCTCTCACCGTTCCAAGTG 1296 TAACTGGGATGCATGGGCAGCCCAGCCCTCTCTCACCGTTCCAAGTGCCGGCCAGTTAAGGCAGAG JAG1 NM_000214 1297 TGGCTTACACTGGCAATGG1298 GCATAGCTGTGAGATGCGG 1299 ACTCGATTTCCCAGCCAACCACAG 1300TGGCTTACACTGGCAATGGTAGTTTCTGTGGTTGGCTG GGAAATCGAGTGCCGCATCTCACAGCTATGCJUN NM_002228 1301 GACTGCAAAGATGGAAACGA 1302 TAGCCATAAGGTCCGCTCTC 1303CTATGACGATGCCCTCAACGCCTC 1304 GACTGCAAAGATGGAAACGACCTTCTATGACGATGCCCTCAACGCCTCGTTCCTCCCGTCCGAGAGCGGACCTTAT GGCTA JUNB NM_002229 1305CTGTCAGCTGCTGCTTGG 1306 AGGGGGTGTCCGTAAAGG 1307 CAAGGGACACGCCTTCTGAACGT1308 CTGTCAGCTGCTGCTTGGGGTCAAGGGACACGCCTTCTGAACGTCCCCTGCCCCTTTACGGACACCCCCT KCNN2 NM_021614 1309TGTGCTATTCATCCCATACCT 1310 GGGCATAGGAGAAGGCAAG 1311TTATACATTCACATGGACGGCCCG 1312 TGTGCTATTCATCCCATACCTGGGAATTATACATTCAC GAATGGCGGCCCGGCTTGCCTTCTCCTATGCCC KCTD12 NM_138444 1313AGCAGTTACTGGCAAGAGGG 1314 TGGAGACCTGAGCAGCCT 1315ACTCTTAGGCGGCAGCGTCCTTTC 1316 AGCAGTTACTGGCAAGAGGGAGAAAGGACGCTGCCGCCTAAGAGTGCAAGGCTGCTCAGGTCTCCA KHDRBS3 NM_006558 1317 CGGGCAAGAAGAGTGGAC1318 CTGTAGACGCCCTTTGCTGT 1319 CAAGACACAAGGCACCTTCAGCGA 1320CGGGCAAGAAGAGTGGACTAACTCAAGACACAAGGCAC CTTCAGCGAGGACAGCAAAGGGCGTCTACAGKIAA0196 NM_014846 1321 CAGACACCAGCTCTGAGGC 1322 AACATTGTGAGGCGGACC 1323TCCCCAGTGTCCAGGCACAGAGTA 1324 CAGACACCAGCTCTGAGGCCAGTTAATCATCCCCAGTGTCCAGGCACAGAGTAGTCGGTCCGCCTCACAATGTT KIAA0247 NM_014734 1325CCGTGGGACATGGAGTGT 1326 GAAGCAAGTCCGTCTCCAAG 1327TCCGCTAGTGATCCTTTGCACCCT 1328 CCGTGGGACATGGAGTGTTCCTTCCGCTAGTGATCCTTTGCACCCTGCTTGGAGACGGACTTGCTTC KIF4A NM_012310 1329 AGAGCTGGTCTCCTCCAAAA1330 GCTGGTCTTGCTCTGTTTCA 1331 CAGGTCAGCAAACTTGAAAGCAGC 1332AGAGCTGGTCTCCTCCAAAATACAGGTCAGCAAACTTG C AAAGCAGCCTGAAACAGAGCAAGACCAGCKIT NM_000222 1333 GAGGCAACTGCTTATGGCTTA 1334 GGCACTCGGCTTGAGCAT 1335TTACAGCGACAGTCATGGCCGCAT 1336 GAGGCAACTGCTTATGGCTTAATTAAGTCAGATGCGGCATTA CATGACTGTCGCTGTAAAGATGCTCAAGCCGAGTGCC KLC1 NM_182923 1337AGTGGCTACGGGATGAACTG 1338 TGAGCCACAGACTGCTCACT 1339CAACACGCAGCAGAAACTGCAGAA 1340 AGTGGCTACGGGATGAACTGGCCAACACGCAGCAGAAAACTGCGAAGAGTGAGCAGTCTGTGGCTCA KLF6 NM_001300 1341 CACGAGACCGGCTACTTCTC1342 GCTCTAGGCAGGTCTGTTGC 1343 AGTACTCCTCCAGAGACGGCAGCG 1344CACGAGACCGGCTACTTCTCGGCGCTGCCGTCTCTGGA GGAGTACTGGCAACAGACCTGCCTAGAGCKLK1 NM_002257 1345 AACACAGCCCAGTTTGTTCA 1346 CCAGGAGGCTCATGTTGAAG 1347TCAGTGAGAGCTTCCCACACCCTG 1348 AACACAGCCCAGTTTGTTCATGTCAGTGAGAGCTTCCCCACACCTGGCTTCAACATGAGCCTCCTGG KLK10 NM_002776 1349 GCCCAGAGGCTCCATCGT1350 CAGAGGTTTGAACAGTGCAG 1351 CCTCTTCCTCCCCAGTCGGCTGA 1352GCCCAGAGGCTCCATCGTCCATCCTCTTCCTCCCCAGT ACACGGCTGAACTCTCCCCTTGTCTGCACTGTTCAAACCTC TG KLK11 NM_006853 1353CACCCCGGCTTCAACAAC 1354 CATCTTCACCAGCATGATGT 1355CCTCCCCAACAAAGACCACCGCA 1356 CACCCCGGCTTCAACAACAGCCTCCCCAACAAAGACCA CACCGCAATGACATCATGCTGGTGAAGATG KLK14 NM_022046 1357 CCCCTAAAATGTTCCTCCTG1358 CTCATCCTCTTGGCTCTGTG 1359 CAGCACTTCAAGTCCTGGCTATAG 1360CCCCTAAAATGTTCCTCCTGCTGACAGCACTTCAAGTC CCACTGGCTATAGCCATGACACAGAGCCAAGAGGATGAG KLK2 NM_005551 1361AGTCTCGGATTGTGGGAGG 1362 TGTACACAGCCACCTGCC 1363TTGGGAATGCTTCTCACACTCCCA 1364 AGTCTCGGATTGTGGGAGGCTGGGAGTGTGAGAAGCATTCCCAACCCTGGCAGGTGGCTGTGTACA KLK3 NM_001648 1365 CCAAGCTTACCACCTGCAC1366 AGGGTGAGGAAGACAACCG 1367 ACCCACATGGTGACACAGCTCTCC 1368CCAAGCTTACCACCTGCACCCGGAGAGCTGTGTCACCA TGTGGGTCCCGGTTGTCTTCCTCACCCTKLRK1 NM_007360 1369 TGAGAGCCAGGCTTCTTGTA 1370 ATCCTGGTCCTCTTTGCTGT 1371TGTCTCAAAATGCCAGCCTTCTGA 1372 TGAGAGCCAGGCTTCTTGTATGTCTCAAAATGCCAGCC ATTCTGAAAGTATACAGCAAAGAGGACCAGGAT KPNA2 NM_002266 1373TGATGGTCCAAATGAACGAA 1374 AAGCTTCACAAGTTGGGGC 1375ACTCCTGTTTTCACCACCATGCCA 1376 TGATGGTCCAAATGAACGAATTGGCATGGTGGTGAAAACAGGAGTTGTGCCCCAACTTGTGAAGCTT KRT1 NM_006121 1377 TGGACAACAACCGCAGTC1378 TATCCTCGTACTGGGCCTTG 1379 CCTCAGCAATGATGCTGTCCAGGT 1380TGGACAACAACCGCAGTCTCGACCTGGACAGCATCATT GCTGAGGTCAAGGCCCAGTACGAGGATAKRT15 NM_002275 1381 GCCTGGTTCTTCAGCAAGAC 1382 CTTGCTGGTCTGGATCATTT 1383TGAACAAAGAGGTGGCCTCCAACA 1384 GCCTGGTTCTTCAGCAAGACTGAGGAGCTGAACAAAGA CGGTGGCCTCCAACACAGAAATGATCCAGACCAGCAAG KRT18 NM_000224 1385AGAGATCGAGGCTCTCAAGG 1386 GGCCTTTTACTTCCTCTTCG 1387TGGTTCTTCTTCATGAAGAGCAGC 1388 AGAGATCGAGGCTCTCAAGGAGGAGCTGCTCTTCATGA TCCAGAAGAACCACGAAGAGGAAGTAAAAGGCC KRT2 NM_000423 1389 CCAGTGACGCCTCTGTGTT1390 GGGCATGGCTAGAAGCAC 1391 ACCTAGACAGCACAGATTCCGCCC 1392CCAGTGACGCCTCTGTGTTCTGGGGCGGAATCTGTGCT GTCTAGGTTTGTGCTTCTAGCCATGCCC KRT5NM_000424 1393 TCAGTGGAGAAGGAGTTGGA 1394 TGCCATATCCAGAGGAAACA 1395CCAGTCAACATCTCTGTTGTCACA 1396 TCAGTGGAGAAGGAGTTGGACCAGTCAACATCTCTGTTAGCA GTCACAAGCAGTGTTTCCTCTGGATATGGCA KRT75 NM_004693 1397TCAAAGTCAGGTACGAAGATG 1398 ACGTCCTTTTTCAGGGCTAC 1399TTCATTCTCAGCAGCTGTGCGCTT 1400 TCAAAGTCAGGTACGAAGATGAAATTAACAAGCGCACAAAATT AA GT GCTGCTGAGAATGAATTTGTAGCCCTGAAAAAGGACGT KRT76 NM_015848 1401ATCTCCAGACTGCTGGTTCC 1402 TCAGGGAATTAGGGGACAGA 1403TCTGGGCTTCAGATCCTGACTCCC 1404 ATCTCCAGACTGCTGGTTCCCAGGGAACCCTCCCTACATCTGGGCTTCAGATCCTGACTCCCTTCTGTCCCCTAAT TCCCTGA KRT8 NM_002273 1405GGATGAAGCTTACATGAACAA 1406 CATATAGCTGCCTGAGGAAG 1407CGTCGGTCAGCCCTTCCAGGC 1408 GGATGAAGCTTACATGAACAAGGTAGAGCTGGAGTCTC GGTAGATTGAT GCCTGGAAGGGCTGACCGACGAGATCAACTTCCTCAGG CAGCTATATG L1CAM NM_0004251409 CTTGCTGGCCAATGCCTA 1410 TGATTGTCCGCAGTCAGG 1411ATCTACGTTGTCCAGCTGCCAGCC 1412 CTTGCTGGCCAATGCCTACATCTACGTTGTCCAGCTGCCAGCCAAGATCCTGACTGCGGACAATCA LAG3 NM_002286 1413 GCCTTAGAGCAAGGGATTCA1414 CGGTTCTTGCTCCAGCTC 1415 TCTATCTTGCTCTGAGCCTGCGGA 1416GCCTTAGAGCAAGGGATTCACCCTCCGCAGGCTCAGAG CAAGATAGAGGAGCTGGAGCAAGAACCGLAMA3 NM_000227 1417 CCTGTCACTGAAGCCTTGG 1418 TGGGTTACTGGTCAGGACAA 1419ATTCAGACTGACAGGCCCCTGGAC 1420 CCTGTCACTGAAGCCTTGGAAGTCCAGGGGCCTGTCAG CTCTGAATGGTTGTCCTGACCAGTAACCCA LAMA4 NM_002290 1421 GATGCACTGCGGTTAGCAG1422 CAGAGGATACGCTCAGCACC 1423 CTCTCCATCGAGGAAGGCAAATCC 1424GATGCACTGCGGTTAGCAGCGCTCTCCATCGAGGAAGG CAAATCCGGGGTGCTGAGCGTATCCTCTGLAMA5 NM_005560 1425 CTCCTGGCCAACAGCACT 1426 ACACAAGGCCCAGCCTCT 1427CTGTTCCTGGAGCATGGCCTCTTC 1428 CTCCTGGCCAACAGCACTGCACTAGAAGAGGCCATGCTCCAGGAACAGCAGAGGCTGGGCCTTGTGT LAMB1 NM_002291 1429 CAAGGAGACTGGGAGGTGTC1430 CGGCAGAACTGACAGTGTTC 1431 CAAGTGCCTGTACCACACGGAAGG 1432CAAGGAGACTGGGAGGTGTCTCAAGTGCCTGTACCACA CGGAAGGGGAACACTGTCAGTTCTGCCGLAMB3 NM_000228 1433 ACTGACCAAGCCTGAGACCT 1434 GTCACACTTGCAGCATTTCA 1435CCACTCGCCATACTGGGTGCAGT 1436 ACTGACCAAGCCTGAGACCTACTGCACCCAGTATGGCGAGTGGCAGATGAAATGCTGCAAGTGTGAC LAMC1 NM_002293 1437 GCCGTGATCTCAGACAGCTAC1438 ACCTGCTTGCCCAAGAACT 1439 CCTCGGTACTTCATTGCTCCTGCA 1440GCCGTGATCTCAGACAGCTACTTTCCTCGGTACTTCAT TGCTCCTGCAAAGTTCTTGGGCAAGCAGGTLAMC2 NM_005562 1441 ACTCAAGCGGAAATTGAAGCA 1442 ACTCCCTGAAGCCGAGACAC1443 AGGTCTTATCAGCACAGTCTCCGC 1444ACTCAAGCGGAAATTGAAGCAGATAGGTCTTATCAGCA T CTCCCAGTCTCCGCCTCCTGGATTCAGTGTCTCGGCTTCAGG GAGT LAPTM5 NM_006762 1445TGCTGGACTTCTGCCTGAG 1446 TGAGATAGGTGGGCACTTCC 1447TCCTGACCCTCTGCAGCTCCTACA 1448 TGCTGGACTTCTGCCTGAGCATCCTGACCCTCTGCAGCTCCTACATGGAAGTGCCCACCTATCTCA LGALS3 NM_002306 1449 AGCGGAAAATGGCAGACAAT1450 CTTGAGGGTTTGGGTTTCCA 1451 ACCCAGATAACGCATCATGGAGCG 1452AGCGGAAAATGGCAGACAATTTTTCGCTCCATGATGCG A TTATCTGGGTCTGGAAACCCAAACCCTCAAGLIG3 NM_002311 1453 GGAGGTGGAGAAGGAGCC 1454 ACAGGTGTCATCAGCGAGG 1455CTGGACGCTCAGAGCTCGTCTCTG 1456 GGAGGTGGAGAAGGAGCCGGGCCAGAGACGAGCTCTGAGCGTCCAGGCCTCGCTGATGACACCTGT LIMS1 NM_004987 1457 TGAACAGTAATGGGGAGCTG1458 TTCTGGGAACTGCTGGAAG 1459 ACTGAGCGCACACGAAACACTGCT 1460TGAACAGTAATGGGGAGCTGTACCATGAGCAGTGTTTC GTGTGCGCTCAGTGCTTCCAGCAGTTCCCAGAALOX NM_002317 1461 CCAATGGGAGAACAACGG 1462 CGCTGAGGCTGGTACTGTG 1463CAGGCTCAGCAAGCTGAACACCTG 1464 CCAATGGGAGAACAACGGGCAGGTGTTCAGCTTGCTGAGCCTGGGCTCACAGTACCAGCCTCAGCG LRP1 NM_002332 1465 TTTGGCCCAATGGGCTAAG1466 GTCTCGATGCGGTCGTAGAA 1467 TCCCGGCTGGGCGCCTCTACT 1468TTTGGCCCAATGGGCTAAGCCTGGACATCCCGGCTGGG GCGCCTCTACTGGGTGGATGCCTTCTACGACCGCATCGA GAC LTBP2 NM_000428 1469GCACACCCATCCTTGAGTCT 1470 GATGGCTGGCCACGTAGT 1471CTTTGCAGCCCTCAGAACTCCAGC 1472 GCACACCCATCCTTGAGTCTCCTTTGCAGCCCTCAGAACTCCAGCCCCACTACGTGGCCAGCCATC LUM NM_002345 1473 GGCTCTTTTGAAGGATTGGTA1474 AAAAGCAGCTGAAACAGCAT 1475 CCTGACCTTCATCCATCTCCAGCA 1476GGCTCTTTTGAAGGATTGGTAAACCTGACCTTCATCCA A CTCTCCAGCACAATCGGCTGAAAGAGGATGCTGTTTCAG CTGCTTTT MAGEA4 NM_002362 1477GCATCTAACAGCCCTGTGC 1478 CAGAGTGAAGAATGGGCCTC 1479CAGCTTCCCTTGCCTCGTGTAACA 1480 GCATCTAACAGCCCTGTGCAGCAGCTTCCCTTGCCTCGTGTAACATGAGGCCCATTCTTCACTCTG MANF NM_006010 1481 CAGATGTGAAGCCTGGAGC1482 AAGGGAATCCCCTCATGG 1483 TTCCTGATGATGCTGGCCCTACAG 1484CAGATGTGAAGCCTGGAGCTTTCCTGATGATGCTGGCC CTACAGTACCCCCATGAGGGGATTCCCTTMAOA NM_000240 1485 GTGTCAGCCAAAGCATGGA 1486 CGACTACGTCGAACATGTGG 1487CCGCGATACTCGCCTTCTCTTGAT 1488 GTGTCAGCCAAAGCATGGAGAATCAAGAGAAGGCGAGTATCGCGGGCCACATGTTCGACGTAGTCG MAP3K5 NM_005923 1489 AGGACCAAGAGGCTACGGA1490 CCTGTGGCCATTTCAATGAT 1491 CAGCCCAGAGACCAGATGTCTGCT 1492AGGACCAAGAGGCTACGGAAAAGCAGCAGACATCTGGTCTCTGGGCTGTACAATCATTGAAATGGCCACAGG MAP3K7 NM_145333 1493CAGGCAAGAACTAGTTGCAGA 1494 CCTGTACCAGGCGAGATGTA 1495TGCTGGTCCTTTTCATCCTGGTCC 1496 CAGGCAAGAACTAGTTGCAGAACTGGACCAGGATGAAA A TAGGACCAGCAAAATACATCTCGCCTGGTACAGG MAP4K4 NM_004834 1497TCGCCGAGATTTCCTGAG 1498 CTGTTGTCTCCGAAGAGCCT 1499AACGTTCCTTGTTCTCCTGCTGCA 1500 TCGCCGAGATTTCCTGAGACTGCAGCAGGAGAACAAGGAACGTTCCGAGGCTCTTCGGAGACAACAG MAP7 NM_003980 1501 GAGGAACAGAGGTGTCTGCAC1502 CTGCCAACTGGCTTTCCA 1503 CATGTACAACAAACGCTCCGGGAA 1504GAGGAACAGAGGTGTCTGCACTTCCATGTACAACAAAC GCTCCGGGAAATGGAAAGCCAGTTGGCAGMAPKAPK3 NM_004635 1505 AAGCTGCAGAGATAATGCGG 1506 GTGGGCAATGTTATGGCTG1507 ATTGGCACTGCCATCCAGTTTCTG 1508AAGCTGCAGAGATAATGCGGGATATTGGCACTGCCATC CAGTTTCTGCACAGCCATAACATTGCCCACMCM2 NM_004526 1509 GACTTTTGCCCGCTACCTTTC 1510 GCCACTAACTGCTTCAGTAT 1511ACAGCTCATTGTTGTCACGCCGGA 1512 GACTTTTGCCCGCTACCTTTCATTCCGGCGTGACAACAGAAGAG ATGAGCTGTTGCTCTTCATACTGAAGCAGTTAGTGGC MCM3 NM_002388 1513GGAGAACAATCCCCTTGAGA 1514 ATCTCCTGGATGGTGATGGT 1515TGGCCTTTCTGTCTACAAGGATCA 1516 GGAGAACAATCCCCTTGAGACAGAATATGGCCTTTCTG CCATCTACAAGGATCACCAGACCATCACCATCCAGGAGAT MCM6 NM_005915 1517TGATGGTCCTATGTGTCACAT 1518 TGGGACAGGAAACACACCAA 1519CAGGTTTCATACCAACACAGGCTT 1520 TGATGGTCCTATGTGTCACATTCATCACAGGTTTCATA TCACAGCAC CCAACACAGGCTTCAGCACTTCCTTTGGTGTGTTTCCT GTCCCA MDK NM_002391 1521GGAGCCGACTGCAAGTACA 1522 GACTTTGGTGCCTGTGCC 1523ATCACACGCACCCCAGTTCTCAAA 1524 GGAGCCGACTGCAAGTACAAGTTTGAGAACTGGGGTGCGTGTGATGGGGGCACAGGCACCAAAGTC MDM2 NM_002392 1525 CTACAGGGACGCCATCGAA1526 ATCCAACCAATCACCTGAAT 1527 CTTACACCAGCATCAAGATCCGG 1528CTACAGGGACGCCATCGAATCCGGATCTTGATGCTGGT GTTGTAAGTGAACATTCAGGTGATTGGTTGGAT MELK NM_014791 1529 AGGATCGCCTGTCAGAAGAG1530 TGCACATAAGCAACAGCAGA 1531 CCCGGGTTGTCTTCCGTCAGATAG 1532AGGATCGCCTGTCAGAAGAGGAGACCCGGGTTGTCTTC CGTCAGATAGTATCTGCTGTTGCTTATGTGCAMET NM_000245 1533 GACATTTCCAGTCCTGCAGTC 1534 CTCCGATCGCACACATTTGT 1535TGCCTCTCTGCCCCACCCTTTGT 1536 GACATTTCCAGTCCTGCAGTCAATGCCTCTCTGCCCCA ACCCTTTGTTCAGTGTGGCTGGTGCCACGACAAATGTGT GCGATCGGAG MGMT NM_002412 1537GTGAAATGAAACGCACCACA 1538 GACCCTGCTCACAACCAGAC 1539 CAGCCCTTTGGGGAAGCTGG1540 GTGAAATGAAACGCACCACACTGGACAGCCCTTTGGGGAAGCTGGAGCTGTCTGGTTGTGAGCAGGGTC MGST1 NM_020300 1541ACGGATCTACCACACCATTGC 1542 TCCATATCCAACAAAAAAAC 1543TTTGACACCCCTTCCCCAGCCA 1544 ACGGATCTACCACACCATTGCATATTTGACACCCCTTCTCAAAG CCCAGCCAAATAGAGCTTTGAGTTTTTTTGTTGGATAT GGA MICA NM_000247 1545ATGGTGAATGTCACCCGC 1546 AAGCCAGAAGCCCTGCAT 1547 CGAGGCCTCAGAGGGCAACATTAC1548 ATGGTGAATGTCACCCGCAGCGAGGCCTCAGAGGGCAACATTACCGTGACATGCAGGGCTTCTGGCTT MKI67 NM_002417 1549 GATTGCACCAGGGCAGAA1550 TCCAAAGTGCCTCTGCTAAG 1551 CCACTCTTCCTTGAACACCCTCCC 1552GATTGCACCAGGGCAGAACAGGGGAGGGTGTTCAAGGA A AGAGTGGCTCTTAGCAGAGGCACTTTGGAMLXIP NM_014938 1553 TGCTTAGCTGGCATGTGG 1554 CAGCCTACTCTCCATGGGC 1555CATGAGATGCCAGGAGACCCTTCC 1556 TGCTTAGCTGGCATGTGGCCGCATGAGATGCCAGGAGACCCTTCCCTGCCCATGGAGAGTAGGCTG MMP11 NM_005940 1557 CCTGGAGGCTGCAACATACC1558 TACAATGGCTTTGGAGGATA 1559 ATCCTCCTGAAGCCCTTTTCGCAG 1560CCTGGAGGCTGCAACATACCTCAATCCTGTCCCAGGCC GCA CGGATCCTCCTGAAGCCCTTTTCGCAGCACTGCTATCCT CCAAAGCCATTGTA MMP2 NM_0045301561 CAGCCAGAAGCGGAAACTTA 1562 AGACACCATCACCTGTGCC 1563AAGTCCGAATCTCTGCTCCCTGCA 1564 CAGCCAGAAGCGGAAACTTAAAAAGTCCGAATCTCTGCTCCCTGCAGGGCACAGGTGATGGTGTCT MMP7 NM_002423 1565 GGATGGTAGCAGTCTAGGGAT1566 GGAATGTCCCATACCCAAAG 1567 CCTGTATGCTGCAACTCATGAACT 1568GGATGGTAGCAGTCTAGGGATTAACTTCCTGTATGCTG TAACT AA TGGCCAACTCATGAACTTGGCCATTCTTTGGGTATGGGACAT TCC MMP9 NM_004994 1569GAGAACCAATCTCACCGACA 1570 CACCCGAGTGTAACCATAGC 1571ACAGGTATTCCTCTGCCAGCTGCC 1572 GAGAACCAATCTCACCGACAGGCAGCTGGCAGAGGAATACCTGTACCGCTATGGTTACACTCGGGTG MPPED2 NM_001584 1573 CCGACCAACCCTCCAATTA1574 AGGGCATTTAGAGCTTCAGG 1575 ATTTGACCTTCCAAACCCACAGGG 1576CCGACCAACCCTCCAATTATATTTGACCTTCCAAACCC A ACAGGGTTCCTGAAGCTCTAAATGCCCTMRC1 NM_002438 1577 CTTGACCTCAGGACTCTGGAT 1578 GGACTGCGGTCACTCCAC 1579CCAACCGCTGTTGAAGCTCAGACT 1580 CTTGACCTCAGGACTCTGGATTGGACTTAACAGTCTGA TGCTTCAACAGCGGTTGGCAGTGGAGTGACCGCAGTCC MRPL13 NM_014078 1581TCCGGTTCCCTTCGTTTAG 1582 GTGGAAAAACTGCGGAAAAC 1583CGGCTGGAAATTATGTCCTCCGTC 1584 TCCGGTTCCCTTCGTTTAGGTCGGCTGGAAATTATGTCCTCCGTCGGTTTTCCGCAGTTTTTCCAC MSH2 NM_000251 1585 GATGCAGAATTGAGGCAGAC1586 TCTTGGCAAGTCGGTTAAGA 1587 CAAGAAGATTTACTTCGTCGATTC 1588GATGCAGAATTGAGGCAGACTTTACAAGAAGATTTACT CCAGATCGTCGATTCCCAGATCTTAACCGACTTGCCAAGA MSH3 NM_002439 1589TGATTACCATCATGGCTCAGA 1590 CTTGTGAAAATGCCATCCAC 1591TCCCAATTGTCGCTTCTTCTGCAG 1592 TGATTACCATCATGGCTCAGATTGGCTCCTATGTTCCTGCAGAAGAAGCGACAATTGGGATTGTGGATGGCATTTT CACAAG MSH6 NM_000179 1593TCTATTGGGGGATTGGTAGG 1594 CAAATTGCGAGTGGTGAAAT 1595CCGTTACCAGCTGGAAATTCCTGA 1596 TCTATTGGGGGATTGGTAGGAACCGTTACCAGCTGGAA GAATTCCTGAGAATTTCACCACTCGCAATTTG MTA1 NM_004689 1597 CCGCCCTCACCTGAAGAGA1598 GGAATAAGTTAGCCGCGCTT 1599 CCCAGTGTCCGCCAAGGAGCG 1600CCGCCCTCACCTGCAGAGAAACGCGCTCCTTGGCGGAC CTACTGGGGGAGGAGAGGAAGAAGCGCGGCTAACTTATTC C MTPN NM_145808 1601GGTGGAAGGAAACCTCTTCA 1602 CAGCAGCAGAAATTCCAGG 1603AAGCTGCCCACAATCTGCTGCATA 1604 GGTGGAAGGAAACCTCTTCATTATGCAGCAGATTGTGGGCAGCTTGAAATCCTGGAATTTCTGCTGCTG MTSS1 NM_014751 1605TTCGACAAGTCCTCCACCAT 1606 CTTGGAACATCCGTCGGTAG 1607CCAAGAAACAGCGACATCAGCCAG 1608 TTCGACAAGTCCTCCACCATTCCAAGAAACAGCGACATCAGCCAGTCCTACCGACGGATGTTCCAAG MUC1 NM_002456 1609 GGCCAGGATCTGTGGTGGTA1610 CTCCACGTCGTGGACATTGA 1611 CTCTGGCCTTCCGAGAAGGTACC 1612GGCCAGGATCTGTGGTGGTACAATTGACTCTGGCCTTC CGAGAAGGTACCATCAATGTCCACGACGTGGAGMVP NM_017458 1613 ACGAGAACGAGGGCATCTATG 1614 GCATGTAGGTGCTTCCAATC 1615CGCACCTTTCCGGTCTTGACATCC 1616 ACGAGAACGAGGGCATCTATGTGCAGGATGTCAAGACC TAC T GGAAAGGTGCGCGCTGTGATTGGAAGCACCTACATGC MYBL2 NM_002466 1617GCCGAGATCGCCAAGATG 1618 CTTTTGATGGTAGAGTTCCA 1619CAGCATTGTCTGTCCTCCCTGGCA 1620 GCCGAGATCGCCAAGATGTTGCCAGGGAGGACAGACAAGTGATTC TGCTGTGAAGAATCACTGGAACTCTACCATCAAAAG MYBPC1 NM_002465 1621CAGCAACCAGGGAGTCTGTA 1622 CAGCAGTAAGTGCCTCCATC 1623AAATTCGCAAGCCCAGCCCCTAT 1624 CAGCAACCAGGGAGTCTGTACCCTGGAAATTCGCAAGCCCAGCCCCTATGATGGAGGCACTTACTGCTG MYC NM_002467 1625 TCCCTCCACTCGGAAGGACTA1626 CGGTTGTTGCTGATCTGTCT 1627 TCTGACACTGTCCAACTTGACCCT 1628TCCCTCCACTCGGAAGGACTATCCTGCTGCCAAGAGGG CA CTTTCAAGTTGGACAGTGTCAGAGTCCTGAGACAGATCAGC AACAACCG MYLK3 NM_182493 1629CACCTGACTGAGCTGGATGT 1630 GATGTAGTGCTGGTGCAGGT 1631CACACCCTCACAGATCTGCCTGGT 1632 CACCTGACTGAGCTGGATGTGGTCCTGTTCACCAGGCAGATCTGTGAGGGTGTGCATTACCTGCACCAGCACTACA TC MYO6 NM_004999 1633AAGCAGTTCTGGAGCAGGAG 1634 GATGAGCTCGGCTTCACTCT 1635CAATCCTCAGGGCCAGCTCCC 1636 AAGCAGTTCTGGAGCAGGAGCGCAGGGACCGGGAGCTGGCCCTGAGGATTGCCCAGAGTGAAGCCGAGCTCATC NCAM1 NM_000615 1637TAGTTCCCAGCTGACCATCA 1638 CAGCCTTGTTCTCAGCAATG 1639CTCAGCCTCGTCGTTCTTATCCAC 1640 TAGTTCCCAGCTGACCATCAAAAAGGTGGATAAGAACG CACGAGGCTGAGTACATCTGCATTGCTGAGAACAAGGCT G NCAPD3 NM_015261 1641TCGTTGCTTAGACAAGGCG 1642 CTCCAGACAGTGTGCAAAGC 1643CTACTGTCCGCAGCAAGGCACTGT 1644 TCGTTGCTTAGACAAGGCGCCTACTGTCCGCAGCAAGGCACTGTCCAGCTTTGCACACTGTCTGGAG NCOR1 NM_006311 1645 AACCGTTACAGCCCAGAATC1646 TCTGGAGAGACCCTTGAACC 1647 CCAGGCTCAGTCTGTCCATCATCA 1648AACCGTTACAGCCCAGAATCCCAGGCTCAGTCTGTCCA TCATCAAAGACCAGGTTCAAGGGTCTCTCCAGANCOR2 NM_006312 1649 CGTCATCTACGAAGGCAAGA 1650 GAGCACTGGGTCACAGACAT 1651CCTCATAGGACAAGACGTGGCCCT 1652 CGTCATCTACGAAGGCAAGAAGGGCCACGTCTTGTCCTATGAGGGTGGCATGTCTGTGACCCAGTGCTC NDRG1 NM_006096 1653 AGGGCAACATTCCACAGC1654 CAGTGCTCCTACTCCGGC 1655 CTGCAAGGACACTCATCACAGCCA 1656AGGGCAACATTCCACAGCTGCCCTGGCTGTGATGAGTG TCCTTGCAGGGGCCGGAGTAGGAGCACTGNDUFS5 NM_004552 1657 AGAAGAGTCAAGGGCACGAG 1658 AGGCCGAACCTTTTCTGG 1659TGTCCAAGAAAGGCATGGCTACCC 1660 AGAAGAGTCAAGGGCACGAGCATCGGGTAGCCATGCCTTTCTTGGACATCCAGAAAAGGTTCGGCCT NEK2 NM_002497 1661 GTGAGGCAGCGCGACTCT1662 TGCCAATGGTGTACAACACT 1663 TGCCTTCCCGGGCTGAGGACT 1664GTGAGGCAGCGCGACTCTGGCGACTGGCCGGCCATGCC TCATTCCCGGGCTGAGGACTATGAAGTGTTGTACACCATTG GCA NETO2 NM_018092 1665CCAGGGCACCATACTGTTTC 1666 AACGGTAAATCAAGGTCTTC 1667AGCCAACCCTTTTCTCCCATCACA 1668 CCAGGGCACCATACTGTTTCCAGCAGCCAACCCTTTTC GTTCCCATCACAACTACGAAGACCTTGATTTACCGTT NEXN NM_144573 1669AGGAGGAGGAAGAAGGTAGCA 1670 GAGCTCCTGATCTGGTTTGC 1671TCATCTTCAGCAGTGGAGCCATTC 1672 AGGAGGAGGAAGAAGGTAGCATCATGAATGGCTCCACT AGCTGAAGATGAAGAGCAAACCAGATCAGGAGCTC NFAT5 NM_006599 1673CTGAACCCCTCTCCTGGTC 1674 AGGAAACGATGGCGAGGT 1675CGAGAATCAGTCCCCGTGGAGTTC 1676 CTGAACCCCTCTCCTGGTCACCGAGAATCAGTCCCCGTGGAGTTCCCCCTCCACCTCGCCATCGTTTCCT NFATC2 NM_173091 1677CAGTCAAGGTCAGAGGCTGAG 1678 CTTTGGCTCGTGGCATTC 1679CGGGTTCCTACCCCACAGTCATTC 1680 CAGTCAAGGTCAGAGGCTGAGCCCGGGTTCCTACCCCACAGTCATTCAGCAGCAGAATGCCACGAGCCAAAG NFKB1 NM_003998 1681CAGACCAAGGAGATGGACCT 1682 AGCTGCCAGTGCTATCCG 1683AAGCTGTAAACATGAGCCGCACCA 1684 CAGACCAAGGAGATGGACCTCAGCGTGGTGCGGCTCATGTTTACAGCTTTTCTTCCGGATAGCACTGGCAGCT NFKBIA NM_020529 1685CTACTGGACGACCGCCAC 1686 CCTTGACCATCTGCTCGTAC 1687CTCGTCTTTCATGGAGTCCAGGCC 1688 CTACTGGACGACCGCCACGACAGCGGCCTGGACTCCAT TGAAAGACGAGGAGTACGAGCAGATGGTCAAGG NME1 NM_000269 1689 CCAACCCTGCAGACTCCAA1690 ATGTATAATGTTCCTGCCAA 1691 CCTGGGACCATCCGTGGAGACTTC 1692CCAACCCTGCAGACTCCAAGCCTGGGACCATCCGTGGA CTTGTATG TGACTTCTGCATACAAGTTGGCAGGAACATTATACAT NNMT NM_006169 1693CCTAGGGCAGGGATGGAG 1694 CTAGTCCAGCCAAACATCCC 1695CCCTCTCCTCATGCCCAGACTCTC 1696 CCTAGGGCAGGGATGGAGAGAGAGTCTGGGCATGAGGAGAGGGTCTCGGGATGTTTGGCTGGACTAG NOS3 NM_000603 1697 ATCTCCGCCTCGCTCATG1698 TCGGAGCCATACAGGATTGT 1699 TTCACTCGCTTCGCCATCACCG 1700ATCTCCGCCTCGCTCATGGGCACGGTGATGGCGAAGCG C AGTGAAGGCGACAATCCTGTATGGCTCCGANOX4 NM_016931 1701 CCTCAACTGCAGCCTTATCC 1702 TGCTTGGAACCTTCTGTGAT 1703CCGAACACTCTTGGCTTACCTCCG 1704 CCTCAACTGCAGCCTTATCCTTTTACCCATGTGCCGAACACTCTTGGCTTACCTCCGAGGATCACAGAAGGTTCCA AGCA NPBWR1 NM_005285 1705TCACCAACCTGTTCATCCTC 1706 GATGTTGATGGGCAGCAC 1707 ATCGCCGACGAGCTCTTCACG1708 TCACCAACCTGTTCATCCTCAACCTGGCCATCGCCGACGAGCTCTTCACGCTGGTGCTGCCCATCAACATC NPM1 NM_002520 1709AATGTTGTCCAGGTTCTATTG 1710 CAAGCAAAGGGTGGAGTTC 1711AACAGGCATTTTGGACAACACATT 1712 AATGTTGTCCAGGTTCTATTGCCAAGAATGTGTTGTCC CCTTG AAAATGCCTGTTTAGTTTTTAAAGATGGAACTCCACCC TTTGCTTG NRG1 NM_013957 1713CGAGACTCTCCTCATAGTGAA 1714 CTTGGCGTGTGGAAATCTAC 1715ATGACCACCCCGGCTCGTATGTCA 1716 CGAGACTCTCCTCATAGTGAAAGGTATGTGTCAGCCATAGGTAT AG GACCACCCCGGCTCGTATGTCACCTGTAGATTTCCACA CGCCAAG NRIP3 NM_0206451717 CCCACAAGCATGAAGGAGA 1718 TGCTCAATCTGGCCCACTA 1719AGCTTTCTCTACCCCGGCATCTCA 1720 CCCACAAGCATGAAGGAGAAAAGCTTTCTCTACCCCGGCATCTCAAAGTAGTGGGCCAGATTGAGCA NRP1 NM_003873 1721 CAGCTCTCTCCACGCGATTC1722 CCCAGCAGCTCCATTCTGA 1723 CAGGATCTACCCCGAGAGAGCCAC 1724CAGCTCTCTCCACGCGATTCATCAGGATCTACCCCGAG TCATAGAGCCACTCATGGCGGACTGGGGCTCAGAATGGAGCT GCTGGG NUP62 NM_153719 1725AGCCTCTTTGCGTCAATAGC 1726 CTGTGGTCACAGGGGTACAG 1727TCATCTGCCACCACTGGACTCTCC 1728 AGCCTCTTTGCGTCAATAGCAACTGCTCCAACCTCATCTGCCACCACTGGACTCTCCCTCTGTACCCCTGTGACCA CAG OAZ1 NM_004152 1729AGCAAGGACAGCTTTGCAGT 1730 GAAGACATGGTCGGCTCG 1731CTGCTCCTCAGCGAACTCCAGGAG 1732 AGCAAGGACAGCTTTGCAGTTCTCCTGGAGTTCGCTGAGGAGCAGCTGCGAGCCGACCATGTCTTC OCLN NM_002538 1733 CCCTCCCATCCGAGTTTC 1734GACGCGGGAGTGTAGGTG 1735 CTCCTCCCTCGGTGACCAATTCAC 1736CCCTCCCATCCGAGTTTCAGGTGAATTGGTCACCGAGGGAGGAGGCCGACACACCACACCTACACTCCCGCGTC ODC1 NM_002539 1737AGAGATCACCGGCGTAATCAA 1738 CGGGCTCAGCTATGATTCTC 1739CCAGCGTTGGACAAATACTTTCCG 1740 AGAGATCACCGGCGTAATCAACCCAGCGTTGGACAAAT ATCA ACTTTCCGTCAGACTCTGGAGTGAGAATCATAGCTGAG CCCG OLFML2B NM_015441 1741CATGTTGGAAGGAGCGTTCT 1742 CACCAGTTTGGTGGTGACTG 1743TGGCCTGGATCTCCTGAAGCTACA 1744 CATGTTGGAAGGAGCGTTCTATGGCCTGGATCTCCTGAAGCTACATTCAGTCACCACCAAACTGGTG OLFML3 NM_020190 1745 TCAGAACTGAGGCCGACAC1746 CCAGATAGTCTACCTCCCGC 1747 CAGACGATCCACTCTCCCGGAGAT 1748TCAGAACTGAGGCCGACACCATCTCCGGGAGAGTGGAT T CGTCTGGAGCGGGAGGTAGACTATCTGGOMD NM_005014 1749 CGCAAACTCAAGACTATCCCA 1750 CAGTCACAGCCTCAATTTCA 1751TCCGATGCACATTCAGCAACTCTA 1752 CGCAAACTCAAGACTATCCCAAATATTCCGATGCACAT TTCC TCAGCAACTCTACCTTCAGTTCAATGAAATTGAGGCTG TGACTG OR51E1 NM_152430 1753GCATGCTTTCAGGCATTGA 1754 AGAAGATGGCCAGCATTTTG 1755TCCTCATCTCCACCTCATCCATGC 1756 GCATGCTTTCAGGCATTGACATCCTCATCTCCACCTCATCCATGCCCAAAATGCTGGCCATCTTCT OR51E2 NM_030774 1757 TATGGTGCCAAAACCAAACA1758 GTCCTTGTCACAGCTGATCT 1759 ACATAGCCAGCACCCGTGTTCTGA 1760TATGGTGCCAAAACCAAACAGATCAGAACACGGGTGCT TGGGCTATGTTCAAGATCAGCTGTGACAAGGAC OSM NM_020530 1761 GTTTCTGAAGGGGAGGTCAC1762 AGGTGTCTGGTTTGGGACA 1763 CTGAGCTGGCCTCCTATGCCTCAT 1764GTTTCTGAAGGGGAGGTCACAGCCTGAGCTGGCCTCCT ATGCCTCATCATGTCCCAAACCAGACACCTPAGE1 NM_003785 1765 CAACCTGACGAAGTGGAATC 1766 CAGATGCTCCCTCATCCTCT 1767CCAACTCAAAGTCAGGATTCTACA 1768 CAACCTGACGAAGTGGAATCACCAACTCAAAGTCAGGACCTGC TTCTACACCTGCTGAAGAGAGAGAGGATGAGGGAGCAT CTG PAGE4 NM_007003 1769GAATCTCAGCAAGAGGAACCA 1770 GTTCTTCGATCGGAGGTGTT 1771CCAACTGACAATCAGGATATTGAA 1772 GAATCTCAGCAAGAGGAACCACCAACTGACAATCAGGACCTGG TATTGAACCTGGACAAGAGAGAGAAGGAACACCTCCGA TCGAAGAAC PAK6 NM_0201681773 CCTCCAGGTCACCCACAG 1774 GTCCCTTCAGGCCAGAACTT 1775AGTTTCAGGAAGGCTGCCCCTCTC 1776 CCTCCAGGTCACCCACAGCCAGTTTCAGGAAGGCTGCCCCTCTCTCCCACTAAGTTCTGGCCTGAAGGGAC PATE1 NM_138294 1777TGGTAATCCCTGGTTAACCTT 1778 TCCACCTTATGCCTTTCACA 1779CAGCACAGTTCTTTAGGCAGCCCA 1780 TGGTAATCCCTGGTTAACCTTCATGGGCTGCCTAAAGA CACTGTGCTGATGTGAAAGGCATAAGGTGGA PCA3 NR_015342 1781 CGTGATTGTCAGGAGCAAGA1782 AGAAAGGGGAGATGCAGAGG 1783 CTGAGATGCTCCCTGCCTTCAGTG 1784CGTGATTGTCAGGAGCAAGACCTGAGATGCTCCCTGCC TTCATGTCGCTCTGCATCTCCCCTTTCTPCDHGB7 NM_018927 1785 CCCAGCGTTGAAGCAGAT 1786 GAAACGCCAGTCCGTGTT 1787ATTCTTAAACAGCAAGCCCCGCC 1788 CCCAGCGTTGAAGCAGATAAGAAGATTCTTAAACAGCAAGCCCCGCCCAACACGGACTGGCGTTTC PCNA NM_002592 1789 GAAGGTGTTGGAGGCACTCAA1790 GGTTTACACCGCTGGAGCTA 1791 ATCCCAGCAGGCCTCGTTGATGAG 1792GAAGGTGTTGGAGGCACTCAAGGACCTCATCAACGAGG G ACCTGCTGGGATATTAGCTCCAGCGGTGTAAACC PDE9A NM_001001570 1793TTCCACAACTTCCGGCAC 1794 AGACTGCAGAGCCAGACCA 1795TACATCATCTGGGCCACGCAGAAG 1796 TTCCACAACTTCCGGCACTGCTTCTGCGTGGCCCAGATGATGTACAGCATGGTCTGGCTCTGCAGTCT PDGFRB NM_002609 1797CCAGCTCTCCTTCCAGCTAC 1798 GGGTGGCTCTCACTTAGCTC 1799ATCAATGTCCCTGTCCGAGTGCTG 1800 CCAGCTCTCCTTCCAGCTACAGATCAATGTCCCTGTCCGAGTGCTGGAGCTAAGTGAGAGCCACCC PECAM1 NM_000442 1801 TGTATTTCAAGACCTCTGTGC1802 TTAGCCTGAGGAATTGCTGT 1803 TTTATGAACCTGCCCTGCTCCCAC 1804TGTATTTCAAGACCTCTGTGCACTTATTTATGAACCTG ACTT GTT ACCCTGCTCCCACAGAACACAGCAATTCCTCAGGCTAA PEX10 NM_153818 1805GGAGAAGTTCCCTCCCCAG 1806 ATCTGTGTCCAGGCCCAC 1807CTACCTTCGGCACTACCGCTGAGC 1808 GGAGAAGTTCCCTCCCCAGAAGCTCATCTACCTTCGGCACTACCGCTGAGCCGGCGCCCGGGTGGGCCTGGACACA GAT PGD NM_002631 1809ATTCCCATGCCCTGTTTTAC 1810 CTGGCTGGAAGCATCTCAT 1811ACTGCCCTCTCCTTCTATGACGGG 1812 ATTCCCATGCCCTGTTTTACCACTGCCCTCTCCTTCTA TTGACGGGTACAGACATGAGATGCTTCCAGCCAG PGF NM_002632 1813 GTGGTTTTCCCTCGGAGC1814 AGCAAGGGAACAGCCTCAT 1815 ATCTTCTCAGACGTCCCGAGCCAG 1816GTGGTTTTCCCTCGGAGCCCCCTGGCTCGGGACGTCTG AGAAGATGCCGGTCATGAGGCTGTTCCCTTGCTPGK1 NM_000291 1817 AGAGCCAGTTGCTGTAGAACT 1818 CTGGGCCTACACAGTCCTTC 1819TCTCTGCTGGGCAAGGATGTTCTG 1820 AGAGCCAGTTGCTGTAGAACTCAAATCTCTGCTGGGCA CAAA TTC AGGATGTTCTGTTCTTGAAGGACTGTGTAGGCCCAG PGR NM_000926 1821GATAAAGGAGCCGCGTGTCA 1822 TCACAAGTCCGGCACTTGAG 1823TAAATTGCCGTCGCAGCCGCA 1824 GATAAAGGAGCCGCGTGTCACTAAATTGCCGTCGCAGCCGCAGCCACTCAAGTGCCGGACTTGTGA PHTF2 NM_020432 1825 GATATGGCTGATGCTGCTCC1826 GGTTTGGGTGTTCTTGTGGA 1827 ACAATCTGGCAATGCACAGTTCCC 1828GATATGGCTGATGCTGCTCCTGGGAACTGTGCATTGCC AGATTGTTTCCACAAGAACACCCAAACCPIK3C2A NM_002645 1829 ATACCAATCACCGCACAAACC 1830 CACACTAGCATTTTCTCCGC1831 TGTGCTGTGACTGGACTTAACAAA 1832ATACCAATCACCGCACAAACCCAGGCTATTTGTTAAGT ATA TAGCCTCCAGTCACAGCACAAAGAAACATATGCGGAGAAAATGC TAGTGTG PIK3CA NM_006218 1833GTGATTGAAGAGCATGCCAA 1834 GTCCTGCGTGGGAATAGC 1835TCCTGCTTCTCGGGATACAGACCA 1836 GTGATTGAAGAGCATGCCAATTGGTCTGTATCCCGAGAAGCAGGATTTAGCTATTCCCACGCAGGAC PIK3CG NM_002649 1837GGAGAACTCAATGTCCATCTC 1838 TGATGCTTAGGCAGGGCT 1839TTCTGGACAATTACTGCCACCCGA 1840 GGAGAACTCAATGTCCATCTCCATTCTTCTGGACAATT CACTGCCACCCGATAGCCCTGCCTAAGCATCA PIM1 NM_002648 1841 CTGCTCAAGGACACCGTCTA1842 GGATCCACTCTGGAGGGC 1843 TACACTCGGGTCCCATCGAAGTCC 1844CTGCTCAAGGACACCGTCTACACGGACTTCGATGGGAC CCGAGTGTATAGCCCTCCAGAGTGGATCCPLA2G7 NM_005084 1845 CCTGGCTGTGGTTTATCCTT 1846 TGACCCATGCTGATGATTTC1847 TGGCAATACATAAATCCTGTTGCC 1848CCTGGCTGTGGTTTATCCTTTTGACTGGCAATACATAA CAATCCTGTTGCCCATATGAAATCATCAGCATGGGTCA PLAU NM_002658 1849GTGGATGTGCCCTGAAGGA 1850 CTGCGGATCCAGGGTAAGAA 1851AAGCCAGGCGTCTACACGAGAGTC 1852 GTGGATGTGCCCTGAAGGACAAGCCAGGCGTCTACACGTCAC AGAGTCTCACACTTCTTACCCTGGATCCGCAG PLAUR NM_002659 1853CCCATGGATGCTCCTCTGAA 1854 CCGGTGGCTACCAGACATTG 1855CATTGACTGCCGAGGCCCCATG 1856 CCCATGGATGCTCCTCTGAAGAGACTTTCCTCATTGACTGCCGAGGCCCCATGAATCAATGTCTGGTAGCCACCGG PLG NM_000301 1857GGCAAAATTTCCAAGACCAT 1858 ATGTATCCATGAGCGTGTGG 1859 TGCCAGGCCTGGGACTCTCA1860 GGCAAAATTTCCAAGACCATGTCTGGACTGGAATGCCAGGCCTGGGACTCTCAGAGCCCACACGCTCATGGATACA T PLK1 NM_005030 1861AATGAATACAGTATTCCCAAG 1862 TGTCTGAAGCATCTTCTGGA 1863 AACCCCGTGGCCGCCTCC1864 AATGAATACAGTATTCCCAAGCACATCAACCCCGTGGC CACAT TGACGCCTCCCTCATCCAGAAGATGCTTCAGACA PLOD2 NM_000935 1865 CAGGGAGGTGGTTGCAAAT1866 TCTCCCAGGATGCATGAAG 1867 TCCAGCCTTTTCGTGGTGACTCAA 1868CAGGGAGGTGGTTGCAAATTTCTAAGGTACAATTGCTCTATTGAGTCACCACGAAAAGGCTGGAGCTTCATGCATC CTGGGAGA PLP2 NM_002668 1869CCTGATCTGCTTCAGTGCC 1870 GCAGCAAGGATCATCTCAAT 1871ACACCAGGCTACTCCTCCCTGTCG 1872 CCTGATCTGCTTCAGTGCCTCCACACCAGGCTACTCCT CCCCTGTCGGTGATTGAGATGATCCTTGCTGC PNLIPRP2 NM_005396 1873TGGAGAAGGTGAACTGCATC 1874 CACGGCTTGGGTGTACATT 1875 ACCCGTGCCTCCAGTCCACAC1876 TGGAGAAGGTGAACTGCATCTGTGTGGACTGGAGGCACGGGTCCCGGGCAATGTACACCCAAGCCGTG POSTN NM_006475 1877 GTGGCCCAATTAGGCTTG1878 TCACAGGTGCCAGCAAAG 1879 TTCTCCATCTGGCCTCAGAGCAGA 1880GTGGCCCAATTAGGCTTGGCATCTGCTCTGAGGCCAGA TGGAGAATACACTTTGCTGGCACCTGTGAPPAP2B NM_003713 1881 ACAAGCACCATCCCAGTGA 1882 CACGAAGAAAACTATGCAGC 1883ACCAGGGCTCCTTGAGCAAATCCT 1884 ACAAGCACCATCCCAGTGATGTTCTGGCAGGATTTGCT AGCAAGGAGCCCTGGTGGCCTGCTGCATAGTTTTCTTCGT G PPFIA3 NM_003660 1885CCTGGAGCTCCGTTACTCTC 1886 AGCCACATAGGGATCCAGG 1887CACCCACTTTACCTTCTGGTGCCC 1888 CCTGGAGCTCCGTTACTCTCAGGCACCCACTTTACCTTCTGGTGCCCACCTGGATCCCTATGTGGCT PPP1R12A NM_002480 1889CGGCAAGGGGTTGATATAGA 1890 TGCCTGGCATCTCTAAGCA 1891CCGTTCTTCTTCCTTTCGAGCTGC 1892 CGGCAAGGGGTTGATATAGAAGCAGCTCGAAAGGAAGAAGAACGGATCATGCTTAGAGATGCCAGGCA PPP3CA NM_000944 1893 ATACTCCGAGCCCACGAA1894 GGAAGCCTGTTGTTTGGC 1895 TACATGCGGTACCCTGCATCTTGG 1896ATACTCCGAGCCCACGAAGCCCAAGATGCAGGGTACCG CATGTACAGGAAAAGCCAAACAACAGGCTTCCPRIMA1 NM_178013 1897 ATCCTCTTCCCTGAGCCG 1898 CCCAGCTGAGAGGGAATTTA 1899TGACGCATCCAGGGCTCTAGTCTG 1900 ATCCTCTTCCCTGAGCCGCTGACGCATCCAGGGCTCTAGTCTGCACATAAATTCCCTCTCAGCTGGG PRKAR1B NM_002735 1901 ACAAAACCATGACTGCGCT1902 TGTCATCCAGGTGAGCGA 1903 AAGGCCATCTCCAAGAACGTGCTC 1904ACAAAACCATGACTGCGCTGGCCAAGGCCATCTCCAAG AACGTGCTCTTCGCTCACCTGGATGACAPRKAR2B NM_002736 1905 TGATAATCGTGGGAGTTTCG 1906 GCACCAGGAGAGGTAGCAGT1907 CGAACTGGCCTTAATGTACAATAC 1908TGATAATCGTGGGAGTTTCGGCGAACTGGCCTTAATGT ACCCAACAATACACCCAGAGCAGCTACAATCACTGCTACCTCT CCTGGTGC PRKCA NM_002737 1909CAAGCAATGCGTCATCAATGT 1910 GTAAATCCGCCCCCTCTTCT 1911CAGCCTCTGCGGAATGGATCACAC 1912 CAAGCAATGCGTCATCAATGTCCCCAGCCTCTGCGGAA TTGGATCACACTGAGAAGAGGGGGCGGATTTAC PRKCB NM_002738 1913 GACCCAGCTCCACTCCTG1914 CCCATTCACGTACTCCATCA 1915 CCAGACCATGGACCGCCTGTACTT 1916GACCCAGCTCCACTCCTGCTTCCAGACCATGGACCGCC TGTACTTTGTGATGGAGTACGTGAATGGGPROM1 NM_006017 1917 CTATGACAGGCATGCCACC 1918 CTCCAACCATGAGGAAGACG 1919ACCCGAGGCTGTGTCTCCAACAC 1920 CTATGACAGGCATGCCACCCCGACCACCCGAGGCTGTGTCTCCAACACCGGAGGCGTCTTCCTCATGGTTGGAG PROS1 NM_000313 1921GCAGCACAGGAATCTTCTTCT 1922 CCCACCTATCCAACCTAATC 1923CTCATCCTGACAGACTGCAGCTGC 1924 GCAGCACAGGAATCTTCTTCTTGGCAGCTGCAGTCTGT TTG CAGGATGAGATATCAGATTAGGTTGGATAGGTGGG PSCA NM_005672 1925ACCGTCATCAGCAAAGGCT 1926 CGTGATGTTCTTCTTGCCC 1927CCTGTGAGTCATCCACGCAGTTCA 1928 ACCGTCATCAGCAAAGGCTGCAGCTTGAACTGCGTGGATGACTCACAGGACTACTACGTGGGCAAGAAGAACATCA CG PSMD13 NM_002817 1929GGAGGAGCTCTACACGAAGAA 1930 CGGATCCTGCACAAAATCA 1931CCTGAAGTGTCAGCTGATGCCACA 1932 GGAGGAGCTCTACACGAAGAAGTTGTGGCATCAGCTGA GCACTTCAGGTGCTTGATTTTGTGCAGGATCCG PTCH1 NM_000264 1933CCACGACAAAGCCGACTAC 1934 TACTCGATGGGCTCTGCTG 1935CCTGAAACAAGGCTGAGAATCCCG 1936 CCACGACAAAGCCGACTACATGCCTGAAACAAGGCTGAGAATCCCGGCAGCAGAGCCCATCGAGTA PTEN NM_000314 1937 TGGCTAAGTGAAGATGACAAT1938 TGCACATATCATTACACCAG 1939 CCTTTCCAGCTTTACAGTGAATTG 1940TGGCTAAGTGAAGATGACAATCATGTTGCAGCAATTCA CATG TTCGT CTGCACTGTAAAGCTGGAAAGGGACGAACTGGTGTAATGATAT GTGCA PTGER3 NM_000957 1941TAACTGGGGCAACCTTTTCT 1942 TTGCAGGAAAAGGTGACTGT 1943CCTTTGCCTTCCTGGGGCTCTT 1944 TAACTGGGGCAACCTTTTCTTCGCCTCTGCCTTTGCCTTCCTGGGGCTCTTGGCGCTGACAGTCACCTTTTCCTGC AA PTGS2 NM_000963 1945GAATCATTCACCAGGCAAATT 1946 CTGTACTGCGGGTGGAACAT 1947CCTACCACCAGCAACCCTGCCA 1948 GAATCATTCACCAGGCAAATTGCTGGCAGGGTTGCTGG GTGGTAGGAATGTTCCACCCGCAGTACAG PTH1R NM_000316 1949 CGAGGTACAAGCTGAGATCAA1950 GCGTGCCTTTCGCTTGAA 1951 CCAGTGCCAGTGTCCAGCGGCT 1952CGAGGTACAAGCTGAGATCAAGAAATCTTGGAGCCGCT GAAGGACACTGGCACTGGACTTCAAGCGAAAGGCACGC PTHLH NM_002820 1953AGTGACTGGGAGTGGGCTAGA 1954 AAGCCTGTTACCGTGAATCG 1955TGACACCTCCACAACGTCGCTGGA 1956 AGTGACTGGGAGTGGGCTAGAAGGGGACCACCTGTCTG A AACACCTCCACAACGTCGCTGGAGCTCGATTCACGGTAA CAGGCTT PTK2 NM_005607 1957GACCGGTCGAATGATAAGGT 1958 CTGGACATCTCGATGACAGC 1959ACCAGGCCCGTCACATTCTCGTAC 1960 GACCGGTCGAATGATAAGGTGTACGAGAATGTGACGGGCCTGGTGAAAGCTGTCATCGAGATGTCCAG PTK2B NM_004103 1961 CAAGCCCAGCCGACCTAAG1962 GAACCTGGAACTGCAGCTTT 1963 CTCCGCAAACCAACCTCCTGGCT 1964CAAGCCCAGCCGACCTAAGTACAGACCCCCTCCGCAAA GCCAACCTCCTGGCTCCAAAGCTGCAGTTCCAGGTTC PTK6 NM_005975 1965GTGCAGGAAAGGTTCACAAA 1966 GCACACACGATGGAGTAAGG 1967AGTGTCTGCGTCCAATACACGCGT 1968 GTGCAGGAAAGGTTCACAAATGTGGAGTGTCTGCGTCCAATACACGCGTGTGCTCCTCTCCTTACTCCATCGTGTG TGC PTK7 NM_002821 1969TCAGAGGACTCACGGTTCG 1970 CATACACCTCCACGCTGTTG 1971CGCAAGGTCCCATTCTTGAAGACC 1972 TCAGAGGACTCACGGTTCGAGGTCTTCAAGAATGGGACCTTGCGCATCAACAGCGTGGAGGTGTATG PTPN1 NM_002827 1973 AATGAGGAAGTTTCGGATGG1974 CTTCGATCACAGCCAGGTAG 1975 CTGATCCAGACAGCCGACCAGCT 1976AATGAGGAAGTTTCGGATGGGGCTGATCCAGACAGCCGACCAGCTGCGCTTCTCCTACCTGGCTGTGATCGAAG PTPRK NM_002844 1977TCAAACCCTCCCAGTGCT 1978 AGCAGCCAGTTCGTCCAG 1979 CCCCATCGTTGTACATTGCAGTGC1980 TCAAACCCTCCCAGTGCTGGCCCCATCGTTGTACATTGCAGTGCTGGTGCTGGACGAACTGGCTGCT PTTG1 NM_004219 1981 GGCTACTCTGATCTATGTTGA1982 GCTTCAGCCCATCCTTAGCA 1983 CACACGGGTGCCTGGTTCTCCA 1984GGCTACTCTGATCTATGTTGATAAGGAAAATGGAGAAC TAAGGAACAGGCACCCGTGTGGTTGCTAAGGATGGGCTGAAGC PYCARD NM_013258 1985CTTTATAGACCAGCACCGGG 1986 AGCATCCAGCAGCCACTC 1987ACGTTTGTGACCCTCGCGATAAGC 1988 CTTTATAGACCAGCACCGGGCTGCGCTTATCGCGAGGGTCACAAACGTTGAGTGGCTGCTGGATGCT RAB27A NM_004580 1989TGAGAGATTAATGGGCATTGT 1990 CCGGATGCTTTATTCGTAGG 1991ACAAATTGCTTCTCACCATCCCCA 1992 TGAGAGATTAATGGGCATTGTGTACAAATTGCTTCTCA GTT CCATCCCCATTAGACCTACGAATAAAGCATCCGG RAB30 NM_014488 1993TAAAGGCTGAGGCACGGA 1994 CTCCCCAGCATCTCATGG 1995 CCATCAGGGCAGTTGCTGATTCCT1996 TAAAGGCTGAGGCACGGAGAAGAAAAGGAATCAGCAACTGCCCTGATGGGCCATGAGATGCTGGGGAG RAB31 NM_006868 1997 CTGAAGGACCCTACGCTCG1998 ATGCAAAGCCAGTGTGCTC 1999 CTTCTCAAAGTGAGGTGCCAGGCC 2000CTGAAGGACCCTACGCTCGGTGGCCTGGCACCTCACTT TGAGAAGAGTGAGCACACTGGCTTTGCATRAD21 NM_006265 2001 TAGGGATGGTATCTGAAACAA 2002 TCGCGTACACCTCTGCTC 2003CACTTAAAACGAATCTCAAGAGGG 2004 TAGGGATGGTATCTGAAACAACAATGGTCACCCTCTTG CATGACCA AGATTCGTTTTAAGTGTAATTCCATAATGAGCAGAGGT GTACGCGA RAD51 NM_0028752005 AGACTACTCGGGTCGAGGTG 2006 AGCATCCGCAGAAACCTG 2007CTTTCAGCCAGGCAGATGCACTTG 2008 AGACTACTCGGGTCGAGGTGAGCTTTCAGCCAGGCAGATGCACTTGGCCAGGTTTCTGCGGATGCT RAD9A NM_004584 2009 GCCATCTTCACCATCAAGG2010 CGGTGTCTGAGAGTGTGGC 2011 CTTTGCTGGACGGCCACTTTGTCT 2012GCCATCTTCACCATCAAGGACTCTTTGCTGGACGGCCA CTTTGTCTTGGCCACACTCTCAGACACCGRAF1 NM_002880 2013 CGTCGTATGCGAGAGTCTGT 2014 TGAAGGCGTGAGGTGTAGAA 2015TCCAGGATGCCTGTTAGTTCTCAG 2016 CGTCGTATGCGAGAGTCTGTTTCCAGGATGCCTGTTAG CATTCTCAGCACAGATATTCTACACCTCACGCCTTCA RAGE NM_014226 2017ATTAGGGGACTTTGGCTCCT 2018 GGGTGGAGATGTATTCCGTG 2019CCGGAGTGTCTATTCCAAGCAGCC 2020 ATTAGGGGACTTTGGCTCCTGCCGGAGTGTCTATTCCAAGCAGCCGTACACGGAATACATCTCCACCC RALA NM_005402 2021 TGGTCCTGAATGTAGCGTGT2022 CCCCATTTCACCTCTTCAAT 2023 TTGTGTTTCTTGGGCAGTCTTTCT 2024TGGTCCTGAATGTAGCGTGTAAGCTTGTGTTTCTTGGG TGAACAGTCTTTCTTGAAATTGAAGAGGTGAAATGGGG RALBP1 NM_006788 2025GGTGTCAGATATAAATGTGCA 2026 TTCGATATTGCCAGCAGCTA 2027TGCTGTCCTGTCGGTCTCAGTACG 2028 GGTGTCAGATATAAATGTGCAAATGCCTTCTTGCTGTCAATGC TAAA TTCA CTGTCGGTCTCAGTACGTTCACTTTATAGCTGCTGGCA ATATCGAA RAP1BNM_001010942 2029 TGACAGCGTGAGAGGTACTAG 2030 CTGAGCCAAGAACGACTAGC 2031CACGCATGATGCAAGCTTGTCAAA 2032 TGACAGCGTGAGAGGTACTAGGTTTTGACAAGCTTGCA GTT TCATGCGTGAGTATAAGCTAGTCGTTCTTGGCTCAG RARB NM_000965 2033ATGAACCCTTGACCCCAAGT 2034 GAGCTGGGTGAGATGCTAGG 2035TGTGCTCTGCTGTGTTCCCACTTG 2036 ATGAACCCTTGACCCCAAGTTCAAGTGGGAACACAGCAGAGCACAGTCCTAGCATCTCACCCAGCTC RASSF1 NM_007182 2037 AGGGCACGTGAAGTCATTG2038 AAAGAGTGCAAACTTGCGG 2039 CACCACCAAGAACTTTCGCAGCAG 2040AGGGCACGTGAAGTCATTGAGGCCCTGCTGCGAAAGTTCTTGGTGGTGGATGACCCCCGCAAGTTTGCACTCTTT RB1 NM_000321 2041CGAAGCCCTTACAAGTTTCC 2042 GGACTCTTCAGGGGTGAAAT 2043CCCTTACGGATTCCTGGAGGGAAC 2044 CGAAGCCCTTACAAGTTTCCTAGTTCACCCTTACGGATTCCTGGAGGGAACATCTATATTTCACCCCTGAAGAGTC C RECK NM_021111 2045GTCGCCGAGTGTGCTTCT 2046 GTGGGATGATGGGTTTGC 2047 TCAAGTGTCCTTCGCTCTTGGCAG2048 GTCGCCGAGTGTGCTTCTGTCAAGTGTCCTTCGCTCTTGGCAGCTGGATGCAAACCCATCATCCCAC REG4 NM_032044 2049 TGCTAACTCCTGCACAGCC2050 TGCTAGGTTTCCCCTCTGAA 2051 TCCTCTTCCTTTCTGCTAGCCTGG 2052TGCTAACTCCTGCACAGCCCCGTCCTCTTCCTTTCTGC CTAGCCTGGCTAAATCTGCTCATTATTTCAGAGGGGAAA CCTAGCA RELA NM_021975 2053CTGCCGGGATGGCTTCTAT 2054 CCAGGTTCTGGAAACTGTGG 2055 CTGAGCTCTGCCCGGACCGCT2056 CTGCCGGGATGGCTTCTATGAGGCTGAGCTCTGCCCGG ATACCGCTGCATCCACAGTTTCCAGAACCTGG RFX1 NM_002918 2057 TCCTCTCCAAGTTCGAGCC2058 CAGGCCCTGGTACAGCAC 2059 TCCAATGGACCAAGCACTGTGACA 2060TCCTCTCCAAGTTCGAGCCCGTGCTCCAATGGACCAAG CACTGTGACAACGTGCTGTACCAGGGCCTGRGS10 NM_001005339 2061 AGACATCCACGACAGCGAT 2062 CCATTTGGCTGTGCTCTTG2063 AGTTCCAGCAGCAGCCACCAGAG 2064 AGACATCCACGACAGCGATGGCAGTTCCAGCAGCAGCCACCAGAGCCTCAAGAGCACAGCCAAATGG RGS7 NM_002924 2065 CAGGCTGCAGAGAGCATTT2066 TTTGCTTGTGCTTCTGCTTG 2067 TGAAAATGAACTCCCACTTCCGGG 2068CAGGCTGCAGAGAGCATTTGCCCGGAAGTGGGAGTTCA TTTTCATGCAAGCAGAAGCACAAGCAAA RHOANM_001664 2069 TGGCATAGCTCTGGGGTG 2070 TGCCACAGCTGCATGAAC 2071AAATGGGCTCAACCAGAAAAGCCC 2072 TGGCATAGCTCTGGGGTGGGCAGTTTTTTGAAAATGGGCTCAACCAGAAAAGCCCAAGTTCATGCAGCTGTGGCA RHOB NM_004040 2073AAGCATGAACAGGACTTGACC 2074 CCTCCCCAAGTCAGTTGC 2075CTTTCCAACCCCTGGGGAAGACAT 2076 AAGCATGAACAGGACTTGACCATCTTTCCAACCCCTGGGGAAGACATTTGCAACTGACTTGGGGAGG RHOC NM_175744 2077 CCCGTTCGGTCTGAGGAA2078 GAGCACTCAAGGTAGCCAAA 2079 TCCGGTTCGCCATGTCCCG 2080CCCGTTCGGTCTGAGGAAGGCCGGGACATGGCGAACCG GG GATCAGTGCCTTTGGCTACCTTGAGTGCTCRLN1 NM_006911 2081 AGCTGAAGGCAGCCCTATC 2082 TTGGAATCCTTTAATGCAGG 2083TGAGAGGCAACCATCATTACCAGA 2084 AGCTGAAGGCAGCCCTATCTGAGAGGCAACCATCATTA TGC CCAGAGCTACAGCAGTATGTACCTGCATTAAAGGATTC CAA RND3 NM_005168 2085TCGGAATTGGACTTGGGAG 2086 CTGGTTACTCCCCTCCAACA 2087TTTTAAGCCTGACTCCTCACCGCG 2088 TCGGAATTGGACTTGGGAGGCGCGGTGAGGAGTCAGGCTTAAAACTTGTTGGAGGGGAGTAACCAG RNF114 NM_018683 2089 TGACAGGGGAAGTGGGTC2090 GGAAGACAGCTTTGGCAAGA 2091 CCAGGTCAGCCCTTCTCTTCCCTT 2092TGACAGGGGAAGTGGGTCCCCAGGTCAGCCCTTCTCTT CCCTTTGGGCTCTTGCCAAAGCTGTCTTCCROBO2 NM_002942 2093 CTACAAGGCCCAGCCAAC 2094 CACCAGTGGCTTTACATTTC 2095CTGTACCATCCACTGCCAGCGTTT 2096 CTACAAGGCCCAGCCAACCAAACGCTGGCAGTGGATGG AGTACAGCGTTACTGAAATGTAAAGCCACTGGTG RRM1 NM_001033 2097GGGCTACTGGCAGCTACATT 2098 CTCTCAGCATCGGTACAAGG 2099CATTGGAATTGCCATTAGTCCCAG 2100 GGGCTACTGGCAGCTACATTGCTGGGACTAATGGCAAT CTCCAATGGCCTTGTACCGATGCTGAGAG RRM2 NM_001034 2101 CAGCGGGATTAAACAGTCCT2102 ATCTGCGTTGAAGCAGTGAG 2103 CCAGCACAGCCAGTTAAAAGATGC 2104CAGCGGGATTAAACAGTCCTTTAACCAGCACAGCCAGT ATAAAAGATGCAGCCTCACTGCTTCAACGCAGAT SWOP NM_005980 2105AGACAAGGATGCCGTGGATAA 2106 GAAGTCCACCTGGGCATCTC 2107TTGCTCAAGGACCTGGACGCCAA 2108 AGACAAGGATGCCGTGGATAAATTGCTCAAGGACCTGGACGCCAATGGAGATGCCCAGGTGGACTTC SAT1 NM_002970 2109 CCTTTTACCACTGCCTGGTT2110 ACAATGCTGTGTCCTTCCG 2111 TCCAGTGCTCTTTCGGCACTTCTG 2112CCTTTTACCACTGCCTGGTTGCAGAAGTGCCGAAAGAG CACTGGACTCCGGAAGGACACAGCATTGTSCUBE2 NM_020974 2113 TGACAATCAGCACACCTGCAT 2114 TGTGACTACAGCCGTGATCC2115 CAGGCCCTCTTCCGAGCGGT 2116 TGACAATCAGCACACCTGCATTCACCGCTCGGAAGAGGTTA GCCTGAGCTGCATGAATAAGGATCACGGCTGTAGTCAC A SDC1 NM_002997 2117GAAATTGACGAGGGGTGTCT 2118 AGGAGCTAACGGAGAACCTG 2119CTCTGAGCGCCTCCATCCAAGG 2120 GAAATTGACGAGGGGTGTCTTGGGCAGAGCTGGCTCTGAGCGCCTCCATCCAAGGCCAGGTTCTCCGTTAGCTCCT SDC2 NM_002998 2121GGATTGAAGTGGCTGGAAAG 2122 ACCAGCCACAGTACCCTCA 2123AACTCCATCTCCTTCCCCAGGCAT 2124 GGATTGAAGTGGCTGGAAAGAGTGATGCCTGGGGAAGGAGATGGAGTTATGAGGGTACTGTGGCTGGT SDHC NM_003001 2125 CTTCCCTCGGGTCTCAGG2126 TTCCCTCCTGGTAAAGGTCA 2127 TTACATCCTCCCTCTCCCCGCAAT 2128CTTCCCTCGGGTCTCAGGCATTTACATCCTCCCTCTCC CCGCAATCTGACCTTTACCAGGAGGGAASEC14L1 NM_001039573 2129 AGGGTTCCCATGTGACCAG 2130 GCAGGCATGCTGTGGAAT2131 CGGGCTTCTACATCCTGCAGTGG 2132 AGGGTTCCCATGTGACCAGGTGGCCGGGCTTCTACATCCTGCAGTGGAAATTCCACAGCATGCCTGC SEC23A NM_006364 2133CGTGTGCATTAGATCAGACAG 2134 CCCATTACCATGTATCCTCC 2135TCCTGGAGATGAAATGCTGTCCCA 2136 CGTGTGCATTAGATCAGACAGGTCTCCTGGAGATGAAA GAG TGCTGTCCCAACCTTACTGGAGGATACATGGTAATGGG SEMA3A NM_006080 2137TTGGAATGCAGTCCGAAGT 2138 CTCTTCATTTCGCCTCTGGA 2139TTGCCAATAGACCAGCGCTCTCTG 2140 TTGGAATGCAGTCCGAAGTCGCAGAGAGCGCTGGTCTATTGGCAATTCCAGAGGCGAAATGAAGAG SEPT9 NM_006640 2141 CAGTGACCACGAGTACCAGG2142 CTTCGATGGTACCCCACTTG 2143 TTGCCAATAGACCAGCGCTCTCTG 2144CAGTGACCACGAGTACCAGGTCAACGGCAAGAGGATCC TTGGGAGGAAGACCAAGTGGGGTACCATCGAAGSERPINA3 NM_001085 2145 GTGTGGCCCTGTCTGCTTA 2146 CCCTGTGCATGTGAGAGCTA2147 AGGGAATCGCTGTCACCTTCCAAG 2148GTGTGGCCCTGTCTGCTTATCCTTGGAAGGTGACAGCG C ATTCCCTGTGTAGCTCTCACATGCACAGGGSERPINB5 NM_002639 2149 CAGATGGCCACTTTGAGAACA 2150 GGCAGCATTAACCACAAGGA2151 AGCTGACAACAGTGTGAACGACCA 2152CAGATGGCCACTTTGAGAACATTTTAGCTGACAACAGT TT TT GACCGTGAACGACCAGACCAAAATCCTTGTGGTTAATGCTGC C SESN3 NM_144665 2153GACCCTGGTTTTGGGTATGA 2154 GAGCTCGGAATGTTGGCA 2155TGCTCTTCTCCTCGTCTGGCAAAG 2156 GACCCTGGTTTTGGGTATGAAGACTTTGCCAGACGAGGAGAAGAGCATTTGCCAACATTCCGAGCTC SFRP4 NM_003014 2157 TACAGGATGAGGCTGGGC2158 GTTGTTAGGGCAAGGGGC 2159 CCTGGGACAGCCTATGTAAGGCCA 2160TACAGGATGAGGCTGGGCATTGCCTGGGACAGCCTATG TAAGGCCATGTGCCCCTTGCCCTAACAACSH3RF2 NM_152550 2161 CCATCACAACAGCCTTGAAC 2162 CACTGGGGTGCTGATCTCTA2163 AACCGGATGGTCCATTCTCCTTCA 2164CCATCACAACAGCCTTGAACACTCTCAACCGGATGGTCCATTCTCCTTCAGGGCGCCATATGGTAGAGATCAGCAC CCCAGTG SH3YL1 NM_015677 2165CCTCCAAAGCCATTGTCAAG 2166 CTTTGAGAGCCAGAGTTCAG 2167CACAGCAGTCATCTGCACCAGTCC 2168 CCTCCAAAGCCATTGTCAAGACCACAGCAGTCATCTGC CACCAGTCCAGCTGAACTCTGGCTCTCAAAG SHH NM_000193 2169 GTCCAAGGCACATATCCACTG2170 GAAGCAGCCTCCCGATTT 2171 CACCGAGTTCTCTGCTTTCACCGA 2172GTCCAAGGCACATATCCACTGCTCGGTGAAAGCAGAGA ACTCGGTGGCGGCCAAATCGGGAGGCTGCTTCSHMT2 NM_005412 2173 AGCGGGTGCTAGAGCTTGTA 2174 ATGGCACTTCGGTCTCCA 2175CCATCACTGCCAACAAGAACACCT 2176 AGCGGGTGCTAGAGCTTGTATCCATCACTGCCAACAAG GAACACCTGTCCTGGAGACCGAAGTGCCAT SIM2 NM_005069 2177 GATGGTAGGAAGGGATGTGC2178 CACAAGGAGCTGTGAATGAG 2179 CGCCTCTCCACGCACTCAGCTAT 2180GATGGTAGGAAGGGATGTGCCCGCCTCTCCACGCACTC G AGCTATACCTCATTCACAGCTCCTTGTGSIPA1L1 NM_015556 2181 CTAGGACAGCTTGGCTTCCA 2182 CATAACCGTAGGGCTCCACA2183 CGCCACAATGCCCTCATAGTTGAC 2184CTAGGACAGCTTGGCTTCCATGTCAACTATGAGGGCAT TGTGGCGGATGTGGAGCCCTACGGTTATGSKIL NM_005414 2185 AGAGGCTGAATATGCAGGACA 2186 CTATCGGCCTCAGCATGG 2187CCAATCTCTGCCTCAGTTCTGCCA 2188 AGAGGCTGAATATGCAGGACAGTTGGCAGAACTGAGGCAGAGATTGGACCATGCTGAGGCCGATAG SLC22A3 NM_021977 2189 ATCGTCAGCGAGTTTGACCT2190 CAGGATGGCTTGGGTGAG 2191 CAGCATCCACGCATTGACACAGAC 2192ATCGTCAGCGAGTTTGACCTTGTCTGTGTCAATGCGTG GATGCTGGACCTCACCCAAGCCATCCTGSLC25A21 NM_030631 2193 AAGTGTTTTTCCCCCTTGAGA 2194 GGCCGATCGATAGTCTCTCT2195 TCATGGTGCTGCATAGCAAATATC 2196AAGTGTTTTTCCCCCTTGAGATAATGGATATTTGCTAT T T CAGCAGCACCATGAAGAAGAGAGACTATCGATCGGCC SLC44A1 NM_080546 2197AGGACCGTAGCTGCACAGAC 2198 ATCCCATCCCAATGCAGA 2199TACCATGGCTGCTGCTCTTCATCC 2200 AGGACCGTAGCTGCACAGACATACCATGGCTGCTGCTCTTCATCCTCTTCTGCATTGGGATGGGAT SMAD4 NM_005359 2201 GGACATTACTGGCCTGTTCAC2202 ACCAATACTCAGGAGCAGGA 2203 TGCATTCCAGCCTCCCATTTCCA 2204GGACATTACTGGCCTGTTCACAATGAGCTTGCATTCCA A TGAGCCTCCCATTTCCAATCATCCTGCTCCTGAGTATTGGT SMARCC2 NM_003075 2205TACCGACTGAACCCCCAA 2206 GACATCACCCGCTAGGTTTC 2207TATCTTACCTCTACCGCCTGCCGC 2208 TACCGACTGAACCCCCAAGAGTATCTTACCTCTACCGCCTGCCGCCGAAACCTAGCGGGTGATGTC SMARCD1 NM_003076 2209 CCGAGTTAGCATATCCCAGG2210 CCTTTGTGCCCAGCTGTC 2211 CCCACCCTTGCTGTGTTGAGTCTG 2212CCGAGTTAGCATATCCCAGGCTCGCAGACTCAACACAG CAAGGGTGGGAGACAGCTGGGCACAAAGG SMONM_005631 2213 GGCATCCAGTGCCAGAAC 2214 CGCGATGTAGCTGTGCAT 2215CTTCACAGAGGCTGAGCACCAGGA 2216 GGCATCCAGTGCCAGAACCCGCTCTTCACAGAGGCTGAGCACCAGGACATGCACAGCTACATCGCG SNAI1 NM_005985 2217 CCCAATCGGAAGCCTAACTA2218 GTAGGGCTGCTGGAAGGTAA 2219 TCTGGATTAGAGTCCTGCAGCTCG 2220CCCAATCGGAAGCCTAACTACAGCGAGCTGCAGGACTC C TAATCCAGAGTTTACCTTCCAGCAGCCCTACSNRPB2 NM_003092 2221 CGTTTCCTGCTTTTGGTTCT 2222 AGGTAGAAGGCGCACGAA 2223CCCACCTAAGGCCTACGCCGACTA 2224 CGTTTCCTGCTTTTGGTTCTTACAGTAGTCGGCGTAGGCCTTAGGTGGGTTCGTGCGCCTTCTACCT SOD1 NM_000454 2225 TGAAGAGAGGCATGTTGGAG2226 AATAGACACATCGGCCACAC 2227 TTTGTCAGCAGTCACATTGCCCAA 2228TGAAGAGAGGCATGTTGGAGACTTGGGCAATGTGACTG CTGACAAAGATGGTGTGGCCGATGTGTCTATTSORBS1 NM_015385 2229 GCAGATGAGTGGAGGCTTTC 2230 AGCGAGTGAAGAGGGCTG 2231ATTTCCATTGGCATCAGCACTGGA 2232 GCAGATGAGTGGAGGCTTTCTTCCAGTGCTGATGCCAATGGAAATGCCCAGCCCTCTTCACTCGCT SOX4 NM_003107 2233 AGATGATCTCGGGAGACTGG2234 GCGCCCTTCAGTAGGTGA 2235 CGAGTCCAGCATCTCCAACCTGGT 2236AGATGATCTCGGGAGACTGGCTCGAGTCCAGCATCTCC AACCTGGTTTTCACCTACTGAAGGGCGCSPARC NM_003118 2237 TCTTCCCTGTACACTGGCAGT 2238 AGCTCGGTGTGGGAGAGGTA2239 TGGACCAGCACCCCATTGACGG 2240 TCTTCCCTGTACACTGGCAGTTCGGCCAGCTGGACCAGTC CACCCCATTGACGGGTACCTCTCCCACACCGAGCT SPARCL1 NM_004684 2241GGCACAGTGCAAGTGATGA 2242 GATTGAGCTCTCTCGGCCT 2243ACTTCATCCCAAGCCAGGCCTTTC 2244 GGCACAGTGCAAGTGATGACTACTTCATCCCAAGCCAGGCCTTTCTGGAGGCCGAGAGAGCTCAATC SPDEF NM_012391 2245 CCATCCGCCAGTATTACAAG2246 GGGTGCACGAACTGGTAGA 2247 ATCATCCGGAAGCCAGACATCTCC 2248CCATCCGCCAGTATTACAAGAAGGGCATCATCCGGAAGCCAGACATCTCCCAGCGCCTCGTCTACCAGTTCGTGCA CCC SPINK1 NM_003122 2249CTGCCATATGACCCTTCCAG 2250 GTTGAAAACTGCACCGCAC 2251ACCACGTCTCTTCAGAAGCCTGGG 2252 CTGCCATATGACCCTTCCAGTCCCAGGCTTCTGAAGAGACGTGGTAAGTGCGGTGCAGTTTTCAAC SPINT1 NM_003710 2253 ATTCCCAGCACAGGCTCTGT2254 AGATGGCTACCACCACCACA 2255 CTGTCGCAGTGTTCCTGGTCATCT 2256ATTCCCAGCACAGGCTCTGTGGAGATGGCTGTCGCAGT A GCGTTCCTGGTCATCTGCATTGTGGTGGTGGTAGCCATCT SPP1 NM_001040058 2257TCACACATGGAAAGCGAGG 2258 GTTCAGGTCCTGGGCAAC 2259TGAATGGTGCATACAAGGCCATCC 2260 TCACACATGGAAAGCGAGGAGTTGAATGGTGCATACAAGGCCATCCCCGTTGCCCAGGACCTGAAC SOLE NM_003129 2261 ATTTTCGAGGCCAAAAAATC2262 CCTGAGCAAGGATATTCACG 2263 TGGGCAAGAAAAACATCTCATTCC 2264ATTTTCGAGGCCAAAAAATCATTTTACTGGGCAAGAAA TTTGAACATCTCATTCCTTTGTCGTGAATATCCTTGCTCAGG SRC NM_005417 2265TGAGGAGTGGTATTTTGGCAA 2266 CTCTCGGGTTCTCTGCATTG 2267AACCGCTCTGACTCCCGTCTGGTG 2268 TGAGGAGTGGTATTTTGGCAAGATCACCAGACGGGAGT GAA CAGAGCGGTTACTGCTCAATGCAGAGAACCCGAGAG SRD5A1 NM_001047 2269GGGCTGGAATCTGTCTAGGA 2270 CCATGACTGCACAATGGCT 2271CCTCTCTCGGAGGCCACAGAGGCT 2272 GGGCTGGAATCTGTCTAGGAGCCCTCTCTCGGAGGCCACAGAGGCTGGGGGTAGCCATTGTGCAGTCATGG SRD5A2 NM_000348 2273GTAGGTCTCCTGGCGTTCTG 2274 TCCCTGGAAGGGTAGGAGTA 2275AGACACCACTCAGAATCCCCAGGC 2276 GTAGGTCTCCTGGCGTTCTGCCAGCTGGCCTGGGGATT ACTGAGTGGTGTCTGCTTAGAGTTTACTCCTACCCTTCC AGGGA ST5 NM_005418 2277CCTGTCCTGCCAGAGCAT 2278 CAGCTGCACAAAACTGGC 2279 AGTCACGAGCACCCAGCGAAACTT2280 CCTGTCCTGCCAGAGCATGGATGAAGTTTCGCTGGGTG CTCGTGACTGGCCAGTTTTGTGCAGCTGSTAT1 NM_007315 2281 GGGCTCAGCTTTCAGAAGTG 2282 ACATGTTCAGCTGGTCCACA 2283TGGCAGTTTTCTTCTGTCACCAAA 2284 GGGCTCAGCTTTCAGAAGTGCTGAGTTGGCAGTTTTCT ATCTGTCACCAAAAGAGGTCTCAATGTGGACCAGCTGAA CATGT STAT3 NM_003150 2285TCACATGCCACTTTGGTGTT 2286 CTTGCAGGAAGCGGCTATAC 2287TCCTGGGAGAGATTGACCAGCA 2288 TCACATGCCACTTTGGTGTTTCATAATCTCCTGGGAGAGATTGACCAGCAGTATAGCCGCTTCCTGCAAG STAT5A NM_003152 2289GAGGCGCTCAACATGAAATTC 2290 GCCAGGAACACGAGGTTCTC 2291CGGTTGCTCTGCACTTCGGCCT 2292 GAGGCGCTCAACATGAAATTCAAGGCCGAAGTGCAGAGCAACCGGGGCCTGACCAAGGAGAACCTCGTGTTCCTGG C STAT5B NM_012448 2293CCAGTGGTGGTGATCGTTCA 2294 GCAAAAGCATTGTCCCAGAG 2295CAGCCAGGACAACAATGCGACGG 2296 CCAGTGGTGGTGATCGTTCATGGCAGCCAGGACAACAA ATGCGACGGCCACTGTTCTCTGGGACAATGCTTTTGC STMN1 NM_005563 2297AATACCCAACGCACAAATGA 2298 GGAGACAATGCAAACCACAC 2299CACGTTCTCTGCCCCGTTTCTTG 2300 AATACCCAACGCACAAATGACCGCACGTTCTCTGCCCCGTTTCTTGCCCCAGTGTGGTTTGCATTGTCTCC STS NM_000351 2301GAAGATCCCTTTCCTCCTACT 2302 GGATGATGTTCGGCCTTGAT 2303CTGCGTGGCTCTCGGCTTCCCA 2304 GAAGATCCCTTTCCTCCTACTGTTCTTTCTGTGGGAAG GTTCCCGAGAGCCACGCAGCATCAAGGCCGAACATCATCC SULF1 NM_015170 2305TGCAGTTGTAGGGAGTCTGG 2306 TCTCAAGAATTGCCGTTGAC 2307TACCGTGCCAGCAGAAGCCAAAG 2308 TGCAGTTGTAGGGAGTCTGGTTACCGTGCCAGCAGAAGCCAAAGAAAGAGTCAACGGCAATTCTTGAGA SUMO1 NM_003352 2309GTGAAGCCACCGTCATCATG 2310 CCTTCCTTCTTATCCCCCAA 2311CTGACCAGGAGGCAAAACCTTCAA 2312 GTGAAGCCACCGTCATCATGTCTGACCAGGAGGCAAAA GTCTGA CCTTCAACTGAGGACTTGGGGGATAAGAAGGAAGG SVIL NM_003174 2313ACTTGCCCAGCACAAGGA 2314 GACACCATCCGTGTCACATC 2315ACCCCAGGACTGATGTCAAGGCAT 2316 ACTTGCCCAGCACAAGGAAGACCCCAGGACTGATGTCAAGGCATACGATGTGACACGGATGGTGTC TAF2 NM_003184 2317 GCGCTCCACTCTCAGTCTTT2318 CTTGTGCTCATGGTGATGGT 2319 AGCCTCCAAACACAGTGACCACCA 2320GCGCTCCACTCTCAGTCTTTACTAAGGAATCTACAGCCTCCAAACACAGTGACCACCATCACCACCATCACCATGA GCACAAG TARP NM_001003799 2321GAGCAACACGATTCTGGGA 2322 GGCACCGTTAACCAGCTAAA 2323TCTTCATGGTGTTCCCCTCCTGG 2324 GAGCAACACGATTCTGGGATCCCAGGAGGGGAACACCA TTGAAGACTAACGACACATACATGAAATTTAGCTGGTTA ACGGTGCC TBP NM_003194 2325GCCCGAAACGCCGAATATA 2326 CGTGGCTCTCTTATCCTCAT 2327 TACCGCAGCAAACCGCTTGGG2328 GCCCGAAACGCCGAATATAATCCCAAGCGGTTTGCTGC GATGGTAATCATGAGGATAAGAGAGCCACG TFDP1 NM_007111 2329 TGCGAAGTGCTTTTGTTTGT2330 GCCTTCCAGACAGTCTCCAT 2331 CGCACCAGCATGGCAATAAGCTTT 2332TGCGAAGTGCTTTTGTTTGTTTGTTTTCGTTTGGTTAAAGCTTATTGCCATGCTGGTGCGGCTATGGAGACTGTCT GGAAGGC TFF1 NM_003225 2333GCCCTCCCAGTGTGCAAAT 2334 CGTCGATGGTATTAGGATAG 2335TGCTGTTTCGACGACACCGTTCG 2336 GCCCTCCCAGTGTGCAAATAAGGGCTGCTGTTTCGACGAAGCA ACACCGTTCGTGGGGTCCCCTGGTGCTTCTATCCTAAT ACCATCGACG TFF3 NM_0032262337 AGGCACTGTTCATCTCAGTTT 2338 CATCAGGCTCCAGATATGAA 2339CAGAAGCGCTTGCCGGGAGCAAAG 2340 AGGCACTGTTCATCTCAGCTTTTCTGTCCCTTTGCTCCTTCT CTTTC G CGGCAAGCGCTTCTGCTGAAAGTTCATATCTGGAGCCT GATG TGFA NM_0032362341 GGTGTGCCACAGACCTTCCT 2342 ACGGAGTTCTTGACAGAGTT 2343TTGGCCTGTAATCACCTGTGCAGC 2344 GGTGTGCCACAGACCTTCCTACTTGGCCTGTAATCACCTTGA CTT TGTGCAGCCTTTTGTGGGCCTTCAAAACTCTGTCAAGA ACTCCGT TGFB1I1NM_001042454 2345 GCTACTTTGAGCGCTTCTCG 2346 GGTCACCATCTTGTGTCGG 2347CAAGATGTGGCTTCTGCAACCAGC 2348 GCTACTTTGAGCGCTTCTCGCCAAGATGTGGCTTCTGCAACCAGCCCATCCGACACAAGATGGTGACC TGFB2 NM_003238 2349 ACCAGTCCCCCAGAAGACTA2350 CCTGGTGCTGTTGTAGATGG 2351 TCCTGAGCCCGAGGAAGTCCC 2352ACCAGTCCCCCAGAAGACTATCCTGAGCCCGAGGAAGTCCCCCCGGAGGTGATTTCCATCTACAACAGCACCAGG TGFB3 NM_003239 2353GGATCGAGCTCTTCCAGATCC 2354 GCCACCGATATAGCGCTGTT 2355CGGCCAGATGAGCACATTGCC 2356 GGATCGAGCTCTTCCAGATCCTTCGGCCAGATGAGCAC TATTGCCAAACAGCGCTATATCGGTGGC TGFBR2 NM_003242 2357 AACACCAATGGGTTCCATCT2358 CCTCTTCATCAGGCCAAACT 2359 TTCTGGGCTCCTGATTGCTCAAGC 2360AACACCAATGGGTTCCATCTTTCTGGGCTCCTGATTGC TCAAGCACAGTTTGGCCTGATGAAGAGGTHBS2 NM_003247 2361 CAAGACTGGCTACATCAGAGT 2362 CAGCGTAGGTTTGGTCATAG2363 TGAGTCTGCCATGACCTGTTTTCC 2364CAAGACTGGCTACATCAGAGTCTTAGTGCATGAAGGAA CTTAGTG ATAGG TTCATAACAGGTCATGGCAGACTCAGGACCTATCTATGACCAA ACCTACGCTG THY1 NM_006288 2365GGACAAGACCCTCTCAGGCT 2366 TTGGAGGCTGTGGGTCAG 2367CAAGCTCCCAAGAGCTTCCAGAGC 2368 GGACAAGACCCTCTCAGGCTGTCCCAAGCTCCCAAGAGCTTCCAGAGCTCTGACCCACAGCCTCCAA TIAM1 NM_003253 2369 GTCCCTGGCTGAAAATGG2370 GGGCTCCCGAAGTCTTCTA 2371 TGGAGCCCTTCTCCCAAGATGGTA 2372GTCCCTGGCTGAAAATGGCCTGGAGCCCTTCTCCCAAG ATGGTACCCTAGAAGACTTCGGGAGCCCTIMP2 NM_003255 2373 TCACCCTCTGTGACTTCATCG 2374 TGTGGTTCAGGCTCTTCTTC2375 CCCTGGGACACCCTGAGCACCA 2376 TCACCCTCTGTGACTTCATCGTGCCCTGGGACACCCTGT TG AGCACCACCCAGAAGAAGAGCCTGAACCACA TIMP3 NM_000362 2377CTACCTGCCTTGCTTTGTGA 2378 ACCGAAATTGGAGAGCATGT 2379CCAAGAACGAGTGTCTCTGGACCG 2380 CTACCTGCCTTGCTTTGTGACTTCCAAGAACGAGTGTCTCTGGACCGACATGCTCTCCAATTTCGGT TK1 NM_003258 2381 GCCGGGAAGACCGTAATTGT2382 CAGCGGCACCAGGTTCAG 2383 CAAATGGCTTCCTCTGGAAGGTCC 2384GCCGGGAAGACCGTAATTGTGGCTGCACTGGATGGGAC CACTTCCAGAGGAAGCCATTTGGGGCCATCCTGAACCTGG TGCCGCTG TMPRSS2 NM_005656 2385GGACAGTGTGCACCTCAAAG 2386 CTCCCACGAGGAAGGTCC 2387AAGCACTGTGCATCACCTTGACCC 2388 GGACAGTGTGCACCTCAAAGACTAAGAAAGCACTGTGCATCACCTTGACCCTGGGGACCTTCCTCGTGGGAG TMPRSS2ERGA DQ204772 2389GAGGCGGAGGGCGAG 2390 ACTGGTCCTCACTCACAACT 2391 TAAGGCTTCCTGCCGCGCTCCA2392 GAGGCGGAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTGGAGCGCGGCAGGAAGCCTTATCAGTTGTGAGTGAGG ACCAGT TMPRSS2ERGB DQ204773 2393GAGGCGGAGGGCGAG 2394 TTCCTCGGGTCTCCAAAGAT 2395 CCTGGAATAACCTGCCGCGC 2396GAGGCGGAGGGCGAGGGGCGGGGAGCGCCGCCTGGAGCGCGGCAGGTTATTCCAGGATCTTTGGAGACCCGAGGAA TNF NM_000594 2397GGAGAAGGGTGACCGACTCA 2398 TGCCCAGACTCGGCAAAG 2399CGCTGAGATCAATCGGCCCGACTA 2400 GGAGAAGGGTGACCGACTCAGCGCTGAGATCAATCGGCCCGACTATCTCGACTTTGCCGAGTCTGGGCA TNFRSF10A NM_003844 2401TGCACAGAGGGTGTGGGTTAC 2402 TCTTCATCTGATTTACAAGC 2403CAATGCTTCCAACAATTTGTTTGC 2404 TGCACAGAGGGTGTGGGTTACACCAATGCTTCCAACAATGTACATG TTGCC TTTGTTTGCTTGCCTCCCATGTACAGCTTGTAAATCAG ATGAAGA TNFRSF10BNM_003842 2405 CTCTGAGACAGTGCTTCGATG 2406 CCATGAGGCCCAACTTCCT 2407CAGACTTGGTGCCCTTTGACTCC 2408 CTCTGAGACAGTGCTTCGATGACTTTGCAGACTTGGTG ACTCCCTTTGACTCCTGGGAGCCGCTCATGAGGAAGTTGGG CCTCATGG TNFRSF18 NM_148901 2409CAGAAGCTGCCAGTTCCC 2410 CACCCACAGGTCTCCCAG 2411 CCTTCTCCTCTGCCGATCGCTC2412 CAGAAGCTGCCAGTTCCCCGAGGAAGAGCGGGGCGAGCGATCGGCAGAGGAGAAGGGGCGGCTGGGAGACCTGTGG GTG TNFSF10 NM_003810 2413CTTCACAGTGCTCCTGCAGTC 2414 CATCTGCTTCAGCTCGTTGG 2415AAGTACACGTAAGTTACAGCCACA 2416 CTTCACAGTGCTCCTGCAGTCTCTCTGTGTGGCTGTAA T TCA CTTACGTGTACTTTACCAACGAGCTGAAGCAGATG TNFSF11 NM_003701 2417AACTGCATGTGGGCTATGG 2418 TGACACCCTCTCCACTTCAG 2419ACATGACCAGGGACCAACCCCTC 2420 AACTGCATGTGGGCTATGGGAGGGGTTGGTCCCTGGTCATGTGCCCCTTCGCAGCTGAAGTGGAGAGGGTGTCA TOP2A NM_001067 2421AATCCAAGGGGGAGAGTGAT 2422 GTACAGATTTTGCCCGAGGA 2423CATATGGACTTTGACTCAGCTGTG 2424 AATCCAAGGGGGAGAGTGATGACTTCCATATGGACTTT GCGACTCAGCTGTGGCTCCTCGGGCAAAATCTGTAC TP53 NM_000546 2425CTTTGAACCCTTGCTTGCAA 2426 CCCGGGACAAAGCAAATG 2427AAGTCCTGGGTGCTTCTGACGCAC 2428 CTTTGAACCCTTGCTTGCAATAGGTGTGCGTCAGAAGC AACCCAGGACTTCCATTTGCTTTGTCCCGGG TP63 NM_003722 2429 CCCCAAGCAGTGCCTCTACA2430 GAATCGCACAGCATCAATAA 2431 CCCGGGTCTCACTGGAGCCCA 2432CCCCAAGCAGTGCCTCTACAGTCAGTGTGGGCTCCAGT CACGAGACCCGGGGTGAGCGTGTTATTGATGCTGTGCGATT C TPD52 NM_005079 2433GCCTGTGAGATTCCTACCTTT 2434 ATGTGCTTGGACCTCGCTT 2435TCTGCTACCCACTGCCAGATGCTG 2436 GCCTGTGAGATTCCTACCTTTGTTCTGCTACCCACTGC GCAGATGCTGCAAGCGAGGTCCAAGCACAT TPM1 NM_001018005 2437TCTCTGAGCTCTGCATTTGTC 2438 GGCTCTAAGGCAGGATGCTA 2439TTCTCCAGCTGACCCTGGTTCTCT 2440 TCTCTGAGCTCTGCATTTGTCTATTCTCCAGCTGACCC CTGGTTCTCTCTCTTAGCATCCTGCCTTAGAGCC TP M2 NM_213674 2441AGGAGATGCAGCTGAAGGAG 2442 CCACCTCTTCATATTTGCGG 2443CCAAGCACATCGCTGAGGATTCAG 2444 AGGAGATGCAGCTGAAGGAGGCCAAGCACATCGCTGAGGATTCAGACCGCAAATATGAAGAGGTGG TPP2 NM_003291 2445 TAACCGTGGCATCTACCTCC2446 ATGCCAACGCCATGATCT 2447 ATCCTGTTCAGGTGGCTGCACCTT 2448TAACCGTGGCATCTACCTCCGAGATCCTGTTCAGGTGG CTGCACCTTCAGATCATGGCGTTGGCAT TPX2NM_012112 2449 TCAGCTGTGAGCTGCGGATA 2450 ACGGTCCTAGGTTTGAGGTT 2451CAGGTCCCATTGCCGGGCG 2452 TCAGCTGTGAGCTGCGGATACCGCCCGGCAATGGGACC AAGATGCTCTTAACCTCAAACCTAGGACCGT TRA2A NM_013293 2453 GCAAATCCAGATCCCAACAC2454 CTTCACGAAGATCCCTCTCT 2455 AACTGAGGCCAAACACTCCAAGGC 2456GCAAATCCAGATCCCAACACTTGCCTTGGAGTGTTTGG GCCTCAGTTTGTACACAACAGAGAGGGATCTTCGTGAAG TRAF3IP2 NM_147200 2457CCTCACAGGAACCGAGCA 2458 CTGGGGCTGGGAATCATA 2459 TGGATCTGCCAACCATAGACACGG2460 CCTCACAGGAACCGAGCAGGCCTGGATCTGCCAACCAT AGACACGGGATATGATTCCCAGCCCCAGTRAM1 NM_014294 2461 CAAGAAAAGCACCAAGAGCC 2462 ATGTCCGCGTGATTCTGC 2463AGTGCTGAGCCACGAATTCGTCC 2464 CAAGAAAAGCACCAAGAGCCCCCCAGTGCTGAGCCACGAATTCGTCCTGCAGAATCACGCGGACAT TRAP1 NM_016292 2465 TTACCAGTGGCTTTCAGATGG2466 TGTCCCGGTTCTAACTCCC 2467 TTCGGCGATTTCAAACACTCCAGA 2468TTACCAGTGGCTTTCAGATGGTTCTGGAGTGTTTGAAA TCGCCGAAGCTTCGGGAGTTAGAACCGGGACATRIM14 NM_033220 2469 CATTCGCCTTAAGGAAAGCA 2470 CAAGGTACCTGGCTTGGTG 2471AACTGCCAGCTCTCAGACCCTTCC 2472 CATTCGCCTTAAGGAAAGCATAAACTGCCAGCTCTCAGACCCTTCCAGCACCAAGCCAGGTACCTTG TRO NM_177556 2473 GCAACTGCCACCCATACAG2474 TGGTGTGGATACTGGCTGTC 2475 CCACCCAAGGCCAAATTACCAATG 2476GCAACTGCCACCCATACAGCTACCACCCAAGGCCAAAT TACCAATGAGACAGCCAGTATCCACACCATRPC6 NM_004621 2477 CGAGAGCCAGGACTATCTGC 2478 TAGCCGTAGCAAGGCAGC 2479CTTCTCCCAGCTCCGAGTCCATG 2480 CGAGAGCCAGGACTATCTGCTCATGGACTCGGAGCTGGGAGAAGACGGCTGCCCGCAAGCCCCGCTGCCTTGCTAC GGCTA TRPV6 NM_018646 2481CCGTAGTCCCTGCAACCTC 2482 TCCTCACTGTTCACACAGGC 2483ACTTTGGGGAGCACCCTTTGTCCT 2484 CCGTAGTCCCTGCAACCTCATCTACTTTGGGGAGCACCCTTTGTCCTTTGCTGCCTGTGTGAACAGTGAGGA TSTA3 NM_003313 2485CAATTTGGACTTCTGGAGGAA 2486 CACCTCAAAGGCCGAGTG 2487AACGTGCACATGAACGACAACGTC 2488 CAATTTGGACTTCTGGAGGAAAAACGTGCACATGAACGACAACGTCCTGCACTCGGCCTTTGAGGTG TUBB2A NM_001069 2489 CGAGGACGAGGCTTAAAAAC2490 ACCATGCTTGAGGACAACAG 2491 TCTCAGATCAATCGTGCATCCTTA 2492CGAGGACGAGGCTTAAAAACTTCTCAGATCAATCGTGC GTGAAATCCTTAGTGAACTTCTGTTGTCCTCAAGCATGGT TYMP NM_001953 2493CTATATGCAGCCAGAGATGTG 2494 CCACGAGTTTCTTACTGAGA 2495ACAGCCTGCCACTCATCACAGCC 2496 CTATATGCAGCCAGAGATGTGACAGCCACCGTGGACAG ACAATGG CCTGCCACTCATCACAGCCTCCATTCTCAGTAAGAAAC TCGTGG TYMS NM_001071 2497GCCTCGGTGTGCCTTTCA 2498 CGTGATGTGCGCAATCATG 2499 CATCGCCAGCTACGCCCTGCTC2500 GCCTCGGTGTGCCTTTCAACATCGCCAGCTACGCCCTG CTCACGTACATGATTGCGCACATCACGUAP1 NM_003115 2501 CTGGAGACGGTCGTAGCTG 2502 GCCAAGCTTTGTAGAAATAG 2503TACCTGTAAACCTTTCTCGGCGCG 2504 CTGGAGACGGTCGTAGCTGCGGTCGCGCCGAGAAAGGT GGTTACAGGTACATACATTACACCCCTATTTCTACAAAGC TTGGC UBE2C NM_007019 2505TGTCTGGCGATAAAGGGATT 2506 ATGGTCCCTACCCATTTGAA 2507TCTGCCTTCCCTGAATCAGACAAC 2508 TGTCTGGCGATAAAGGGATTTCTGCCTTCCCTGAATCA CGACAACCTTTTCAAATGGGTAGGGACCAT UBE2G1 NM_003342 2509 TGACACTGAACGAGGTGGC2510 AAGCAGAGAGGAATCGCCT 2511 TTGTCCCACCAGTGCCTCATCAGT 2512TGACACTGAACGAGGTGGCTTTTGTCCCACCAGTGCCT CATCAGTGTGAGGCGATTCCTCTCTGCTTUBE2T NM_014176 2513 TGTTCTCAAATTGCCACCAA 2514 AGAGGTCAACACAGTTGCGA 2515AGGTGCTTGGAGACCATCCCTCAA 2516 TGTTCTCAAATTGCCACCAAAAGGTGCTTGGAGACCATCCCTAACATCGCAACTGTGTTGACCTCTC UGDH NM_003359 2517 GAAACTCCAGAGGGCCAGA2518 CTCTGGGAACCCAGTGCTC 2519 TATACAGCACACAGGGCCTGCACA 2520GAAACTCCAGAGGGCCAGAGAGCTGTGCAGGCCCTGTG TGCTGTATATGAGCACTGGGTTCCCAGAGUGT2B15 NM_001076 2521 AAGCCTGAAGTGGAATGACTG 2522 CCTCCATTTAAAACCCTCCA2523 AAAGATGGGACTCCTCCTTTATTT 2524AAGCCTGAAGTGGAATGACTGAAAGATGGGACTCCTCC CAGCATTTATTTCAGCATGGAGGGTTTTAAATGGAGG UGT2B17 NM_001077 2525TTGAGTTTGTCATGCGCC 2526 TCCAGGTGAGGTTGTGGG 2527 ACCCGAAGGTGCTTGGCTCCTTTA2528 TTGAGTTTGTCATGCGCCATAAAGGAGCCAAGCACCTT CGGGTCGCAGCCCACAACCTCACCTGGAUHRF1 NM_013282 2529 CTACAGGGGCAAACAGATGG 2530 GGTGTCATTCAGGCGGAC 2531CGGCCATACCCTCTTCGACTACGA 2532 CTACAGGGGCAAACAGATGGAGGACGGCCATACCCTCTTCGACTACGAGGTCCGCCTGAATGACACC UTP23 NM_032334 2533 GATTGCACAAAAATGCCAAG2534 GGAAAGCAGACATTCTGATC 2535 TCGAAATTGTCCTCATTTCAAGAA 2536GATTGCACAAAAATGCCAAGTTCGAAATTGTCCTCATT C TGCATCAAGAATGCAGTGAGTGGATCAGAATGTCTGCTTTCC VCAM1 NM_001078 2537TGGCTTCAGGAGCTGAATACC 2538 TGCTGTCGTGATGAGAAAAT 2539CAGGCACACACAGGTGGGACACAA 2540 TGGCTTCAGGAGCTGAATACCCTCCCAGGCACACACAGAGTG AT GTGGGACACAAATAAGGGTTTTGGAACCACTATTTTCT CATCACGACAGCA VCLNM_003373 2541 GATACCACAACTCCCATCAAG 2542 TCCCTGTTAGGCGCATCAG 2543AGTGGCAGCCACGGCGCC 2544 GATACCACAACTCCCATCAAGCTGTTGGCAGTGGCAGC CTCACGGCGCCTCCTGATGCGCCTAACAGGGA VCPIP1 NM_025054 2545TTTCTCCCAGTACCATTCGTG 2546 TGAATAGGGAGCCTTGGTAG 2547TGGTCCATCCTCTGCACCTGCTAC 2548 TTTCTCCCAGTACCATTCGTGATGGTCCATCCTCTGCA GCCTGCTACACCTACCAAGGCTCCCTATTCA VDR NM_000376 2549 CCTCTCCTTCCAGCCTGAGT2550 TCATTGCCAAACACTTCGAG 2551 CAGCATGAAGCTAACGCCCCTTGT 2552CCTCTCCTTCCAGCCTGAGTGCAGCATGAAGCTAACGC CCCTTGTGCTCGAAGTGTTTGGCAATGAVEGFA NM_003376 2553 CTGCTGTCTTGGGTGCATTG 2554 GCAGCCTGGGACCACTTG 2555TTGCCTTGCTGCTCTACCTCCACC 2556 CTGCTGTCTTGGGTGCATTGGAGCCTTGCCTTGCTGCT ACTACCTCCACCATGCCAAGTGGTCCCAGGCTGC VEGFB NM_003377 2557TGACGATGGCCTGGAGTGT 2558 GGTACCGGATCATGAGGATC 2559 CTGGGCAGCACCAAGTCCGGA2560 TGACGATGGCCTGGAGTGTGTGCCCACTGGGCAGCACC TGAAGTCCGGATGCAGATCCTCATGATCCGGTACC VEGFC NM_005429 2561CCTCAGCAAGACGTTATTTGA 2562 AAGTGTGATTGGCAAAACTG 2563CCTCTCTCTCAAGGCCCCAAACCA 2564 CCTCAGCAAGACGTTATTTGAAATTACAGTGCCTCTCTAATT ATTG GT CTCAAGGCCCCAAACCAGTAACAATCAGTTTTGCCAAT CACACTT VIMNM_003380 2565 TGCCCTTAAAGGAACCAATGA 2566 GCTTCAACGGCAAAGTTCTC 2567ATTTCACGCATCTGGCGTTCCA 2568 TGCCCTTAAAGGAACCAATGAGTCCCTGGAACGCCAGA TTTGCGTGAAATGGAAGAGAACTTTGCCGTTGAAGC VTHB NM_006370 2569ACGTTATGCACCCCTGTCTT 2570 CCGATGGAGTTTAGCAAGGT 2571CGAAACCCCATGATGTCTAAGCTT 2572 ACGTTATGCACCCCTGTCTTTCCGAAACCCCATGATGT CGCTAAGCTTCGAAACTACCGGAAGGACCTTGCTAAACTC CATCGG WDR19 NM_025132 2573GAGTGGCCCAGATGTCCATA 2574 GATGCTTGAGGGCTTGGTT 2575CCCCTCGACGTATGTCTCCCATTC 2576 GAGTGGCCCAGATGTCCATAAGAATGGGAGACATACGTCGAGGGGTTAACCAAGCCCTCAAGCATC WFDC1 NM_021197 2577 ACCCCTGCTCTGTCCCTC2578 ATACCTTCGGCCACGTCAC 2579 CTATGAGTGCCACATCCTGAGCCC 2580ACCCCTGCTCTGTCCCTCGGGCTATGAGTGCCACATCC TGAGCCCAGGTGACGTGGCCGAAGGTATWISP1 NM_003882 2581 AGAGGCATCCATGAACTTCAC 2582 CAAACTCCACAGTACTTGGG2583 CGGGCTGCATCAGCACACGC 2584 AGAGGCATCCATGAACTTCACACTTGCGGGCTGCATCA ATTGA GCACACGCTCCTATCAACCCAAGTACTGTGGAGTTTG WNT5A NM_003392 2585GTATCAGGACCACATGCAGTA 2586 TGTCGGAATTGATACTGGCA 2587TTGATGCCTGTCTTCGCGCCTTCT 2588 GTATCAGGACCACATGCAGTACATCGGAGAAGGCGCGACATC TT AGACAGGCATCAAAGAATGCCAGTATCAATTCCGACA wwox NM_016373 2589ATCGCAGCTGGTGGGTGTAC 2590 AGCTCCCTGTTGCATGGACT 2591CTGCTGTTTACCTTGGCGAGGCCT 2592 ATCGCAGCTGGTGGGTGTACACACTGCTGTTTACCTTG TTTC GCGAGGCCTTTCACCAAGTCCATGCAACAGGGAGCT XIAP NM_001167 2593GCAGTTGGAAGACACAGGAAA 2594 TGCGTGGCACTATTTTCAAG 2595TCCCCAAATTGCAGATTTATCAAC 2596 GCAGTTGGAAGACACAGGAAAGTATCCCCAAATTGCAG GTA GGC ATTTATCAACGGCTTTTATCTTGAAAATAGTGCCACGC A XRCC5 NM_021141 2597AGCCCACTTCAGCGTCTC 2598 AGCAGGATTCACACTTCCAA 2599TCTGGCTGAAGGCAGTGTCACCTC 2600 AGCCCACTTCAGCGTCTCCAGTCTGGCTGAAGGCAGTG CTCACCTCTGTTGGAAGTGTGAATCCTGCT YY1 NM_003403 2601 ACCCGGGCAACAAGAAGT 2602GACCGAGAACTCGCCCTC 2603 TTGATCTGCACCTGCTTCTGCTCC 2604ACCCGGGCAACAAGAAGTGGGAGCAGAAGCAGGTGCAG ATCAAGACCCTGGAGGGCGAGTTCTCGGTCZFHX3 NM_006885 2605 CTGTGGAGCCTCTGCCTG 2606 GGAGCAGGGTTGGATTGAG 2607ACCTGGCCCAACTCTACCAGCATC 2608 CTGTGGAGCCTCTGCCTGCGGACCTGGCCCAACTCTACCAGCATCAGCTCAATCCAACCCTGCTCC ZFP36 NM_003407 2609 CATTAACCCACTCCCCTGA2610 CCCCCACCATCATGAATACT 2611 CAGGTCCCCAAGTGTGCAAGCTC 2612CATTAACCCACTCCCCTGACCTCACGCTGGGGCAGGTCCCCAAGTGTGCAAGCTCAGTATTCATGATGGTGGGGG ZMYND8 NM_183047 2613GGTCTGGGCCAAACTGAAG 2614 TGCCCGTCTTTATCCCTTAG 2615CTTTTGCAGGCCAGAATGGAAACC 2616 GGTCTGGGCCAAACTGAAGGGGTTTCCATTCTGGCCTGCAAAAGCTCTAAGGGATAAAGACGGGCA ZNF3 NM_017715 2617 CGAAGGGACTCTGCTCCA 2618GCAGGAGGTCCTCAGAAGG 2619 AGGAGGTTCCACACTCGCCAGTTC 2620CGAAGGGACTCTGCTCCAGTGAACTGGCGAGTGTGGAA CCTCCTGACACCTTCTGAGGACCTCCTGCZNF827 NM_178835 2621 TGCCTGAGGACCCTCTACC 2622 GAGGTGGCGGAGTGACTTT 2623CCCGCCTTCAGAGAAGAAACCAGA 2624 TGCCTGAGGACCCTCTACCGCCCCCGCCTTCAGAGAAGAAACCAGAAAAAGTCACTCCGCCACCTC ZWINT NM_007057 2625 TAGAGGCCATCAAAATTGGC2626 TCCGTTTCCTCTGGGCTT 2627 ACCAAGGCCCTGACTCAGATGGAG 2628TAGAGGCCATCAAAATTGGCCTCACCAAGGCCCTGACT CAGATGGAGGAAGCCCAGAGGAAACGGA

TABLE B SEQ ID microRNA Sequence NO hsa-miR-1 UGGAAUGUAAAGAAGUAUGUAU2629 hsa-miR-103 GCAGCAUUGUACAGGGCUAUGA 2630 hsa-miR-106bUAAAGUGCUGACAGUGCAGAU 2631 hsa-miR-lOa UACCCUGUAGAUCCGAAUUUGUG 2632hsa-miR-133a UUUGGUCCCCUUCAACCAGCUG 2633 hsa-miR-141UAACACUGUCUGGUAAAGAUGG 2634 hsa-miR-145 GUCCAGUUUUCCCAGGAAUCCCU 2635hsa-miR-146b-5p UGAGAACUGAAUUCCAUAGGCU 2636 hsa-miR-150UCUCCCAACCCUUGUACCAGUG 2637 hsa-miR-152 UCAGUGCAUGACAGAACUUGG 2638hsa-miR-155 UUAAUGCUAAUCGUGAUAGGGGU 2639 hsa-miR-182UUUGGCAAUGGUAGAACUCACACU 2640 hsa-miR-191 CAACGGAAUCCCAAAAGCAGCUG 2641hsa-miR-19b UGUAAACAUCCUCGACUGGAAG 2642 hsa-miR-200cUAAUACUGCCGGGUAAUGAUGGA 2643 hsa-miR-205 UCCUUCAUUCCACCGGAGUCUG 2644hsa-miR-206 UGGAAUGUAAGGAAGUGUGUGG 2645 hsa-miR-21UAGCUUAUCAGACUGAUGUUGA 2646 hsa-miR-210 CUGUGCGUGUGACAGCGGCUGA 2647hsa-miR-22 AAGCUGCCAGUUGAAGAACUGU 2648 hsa-miR-222 AGCUACAUCUGGCUACUGGGU2649 hsa-miR-26a UUCAAGUAAUCCAGGAUAGGCU 2650 hsa-miR-27aUUCACAGUGGCUAAGUUCCGC 2651 hsa-miR-27b UUCACAGUGGCUAAGUUCUGC 2652hsa-miR-29b UAGCACCAUUUGAAAUCAGUGUU 2653 hsa-miR-30aCUUUCAGUCGGAUGUUUGCAGC 2654 hsa-miR-30e-5p CUUUCAGUCGGAUGUUUACAGC 2655hsa-miR-31 AGGCAAGAUGCUGGCAUAGCU 2656 hsa-miR-331 GCCCCUGGGCCUAUCCUAGAA2657 hsa-miR-425 AAUGACACGAUCACUCCCGUUGA 2658 hsa-miR-449aUGGCAGUGUAUUGUUAGCUGGU 2659 hsa-miR-486-5p UCCUGUACUGAGCUGCCCCGAG 2660hsa-miR-92a UAUUGCACUUGUCCCGGCCUGU 2661 hsa-miR-93CAAAGUGCUGUUCGUGCAGGUAG 2662 hsa-miR-99a AACCCGUAGAUCCGAUCUUGUG 2663

What is claimed is:
 1. A method for determining a likelihood of cancerrecurrence in a patient with prostate cancer, comprising: measuring anexpression level of at least one gene in a biological sample comprisingprostate tissue obtained from the patient, wherein the at least one genecomprises a gene from Tables 3A, 3B, 4A, 4B, 5A, 5B, 6A, 6B, 7A, 7B, 8A,8B, 10A, or 10B, or genes that co-express with the at least one gene;predicting a likelihood of cancer recurrence for the patient; wherein anexpression level of any gene in Tables 3A, 4A, 5A, 6A, 7A, 8A, and 10Ais positively associated with an increased risk of recurrence, andwherein an expression level of any gene in Tables 3B, 4B, 5B, 6B, 7B 8B,and 10B is negatively associated with a increased risk of recurrence. 2.The method of claim 1, wherein said expression level is measured usingan RNA transcript of the at least one gene.
 3. The method of claim 1,wherein said expression is measured using an oligonucleotide associatedwith the at least one gene.
 4. The method of claim 1, further comprisingnormalizing said expression level to obtain a normalized expressionlevel.
 5. The method of claim 1, further comprising generating a reportbased on the Recurrence Score (RS).
 6. The method of claim 5, whereinthe report comprises an estimate of recurrence risk based on clinicalrecurrence-free interval (cRFI).
 7. The method of claim 5, wherein theRS is based on a biochemical recurrence-free interval (bRFI).
 8. Themethod of claim 1, wherein the biological sample has a positive TMPRSS2fusion status.
 9. The method of claim 1, wherein the biological samplehas a negative TMPRSS2 fusion status.
 10. The method of claim 1, whereinthe patient has early-stage prostate cancer.
 11. The method of claim 1,wherein the biological sample comprises prostate tumor tissue with theprimary Gleason pattern for said prostate tumor.
 12. The method of claim1, wherein the biological samples comprises prostate tumor tissue withthe highest Gleason pattern for said prostate tumor.
 13. The method ofclaim 1, wherein the biological sample is prostate tumor tissue.
 14. Themethod of claim 1, wherein the biological sample is non-tumor prostatetissue.
 15. The method of claim 1, further comprising classifying thepatient as TMPRSS2 fusion positive or negative, wherein an expressionlevel of any gene in Table 9A is associated with a positive TMPRSS2fusion status, and wherein an expression level of any gene in Table 9Bis associated with a negative TMPRSS2 fusion status.
 16. The method ofclaim 1, wherein the biological sample comprises non-tumor prostatetissue, and wherein the at least one gene comprises a gene from Tables10A or 10B.
 17. A method for determining a likelihood of upgrading orupstaging in a patient with prostate cancer, comprising: measuring anexpression level of at least one gene in a biological sample comprisingprostate tissue obtained from the patient, wherein the at least one genecomprises a gene from Table 13A or 13B, or genes that co-express withthe at least one gene; wherein an expression level of any gene in Tables13A is positively associated with an increased risk ofupgrading/upstaging, and wherein an expression level of any gene inTable 13B is negatively associated with a increased risk ofupgrading/upstaging.
 18. A method for determining a likelihood of cancerrecurrence in a patient with prostate cancer, comprising: measuring anexpression level of at least one microRNA in a biological samplecomprising prostate tissue obtained from the patient, wherein the atleast one microRNA is a microRNA selected from hsa-miR-93; hsa-miR-106b;hsa-miR-21; hsa-miR-449a; hsa-miR-182; hsa-miR-27a; hsa-miR-103;hsa-miR-141; hsa-miR-92a; hsa-miR-22; hsa-miR-29b; hsa-miR-210;hsa-miR-331; hsa-miR-191; hsa-miR-425; hsa-miR-200c; hsa-miR-30e-5p;hsa-miR-133a; hsa-miR-30a; hsa-miR-222; hsa-miR-1; hsa-miR-145;hsa-miR-486-5p; hsa-miR-19b; hsa-miR-205; hsa-miR-31; hsa-miR-155;hsa-miR-206; hsa-miR-99a; and hsa-miR-146b-5p; and normalizing saidexpression level to obtain a normalized expression level; wherein anormalized expression level of hsa-miR-93; hsa-miR-106b; hsa-miR-21;hsa-miR-449a; hsa-miR-182; hsa-miR-27a; hsa-miR-103; hsa-miR-141;hsa-miR-92a; hsa-miR-22; hsa-miR-29b; hsa-miR-210; hsa-miR-331;hsa-miR-191; hsa-miR-425; and hsa-miR-200c is positively associated withan increased risk of recurrence; and wherein a normalized expressionlevel of hsa-miR-30e-5p; hsa-miR-133a; hsa-miR-30a; hsa-miR-222;hsa-miR-1; hsa-miR-145; hsa-miR-486-5p; hsa-miR-19b; hsa-miR-205;hsa-miR-31; hsa-miR-155; hsa-miR-206; hsa-miR-99a; and hsa-miR-146b-5pis negatively associated with an increased risk of recurrence.
 19. Themethod of claim 18, further comprising measuring an expression level ofat least one gene in said biological sample.
 20. The method of claim 19,wherein the at least one gene is a gene selected from Tables 3A, 3B, 4A,4B, 5A, 5B, 6A, 6B, 7A, 7B, 8A, 8B, 10A, or 10B, or genes thatco-express with the at least one gene; wherein an expression level ofany gene in Tables 3A, 4A, 5A, 6A, 7A, 8A, and 10A is positivelyassociated with an increased risk of recurrence, and wherein anexpression level of any gene in Tables 3B, 4B, 5B, 6B, 7B 8B, and 10B isnegatively associated with a increased risk of recurrence.